From 6bfc23e9234309107d2f212ff37be1bc2bd17d7d Mon Sep 17 00:00:00 2001 From: Adrian Zimmer Date: Sat, 25 Dec 2021 12:22:15 +0100 Subject: [PATCH] Add autogenerated documentation (#10) --- docs/.nojekyll | 1 + docs/assets/highlight.css | 85 + docs/assets/icons.css | 1043 +++++++++++++ docs/assets/icons.png | Bin 0 -> 9615 bytes docs/assets/icons@2x.png | Bin 0 -> 28144 bytes docs/assets/main.js | 52 + docs/assets/search.js | 1 + docs/assets/style.css | 1388 +++++++++++++++++ docs/assets/widgets.png | Bin 0 -> 480 bytes docs/assets/widgets@2x.png | Bin 0 -> 855 bytes docs/classes/ArraySchema.html | 20 + docs/classes/CommandInputArraySchema.html | 28 + docs/classes/CommandInputEnumSchema.html | 28 + docs/classes/CommandInputParameter.html | 102 ++ docs/classes/CommandInputRecordField.html | 95 ++ docs/classes/CommandInputRecordSchema.html | 28 + docs/classes/CommandLineBindable.html | 18 + docs/classes/CommandLineBinding.html | 92 ++ docs/classes/CommandLineTool.html | 113 ++ 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+ +.tsd-kind-signature > .tsd-kind-icon:before { + background-position: 0px -153px; +} +.tsd-kind-signature.tsd-is-protected > .tsd-kind-icon:before { + background-position: -17px -153px; +} +.tsd-kind-signature.tsd-is-private > .tsd-kind-icon:before { + background-position: -34px -153px; +} + +.tsd-kind-type-alias > .tsd-kind-icon:before { + background-position: 0px -170px; +} +.tsd-kind-type-alias.tsd-is-protected > .tsd-kind-icon:before { + background-position: -17px -170px; +} +.tsd-kind-type-alias.tsd-is-private > .tsd-kind-icon:before { + background-position: -34px -170px; +} + +.tsd-kind-type-alias.tsd-has-type-parameter > .tsd-kind-icon:before { + background-position: 0px -187px; +} +.tsd-kind-type-alias.tsd-has-type-parameter.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -17px -187px; +} +.tsd-kind-type-alias.tsd-has-type-parameter.tsd-is-private + > .tsd-kind-icon:before { + background-position: -34px -187px; +} + +.tsd-kind-variable > .tsd-kind-icon:before { + background-position: -136px -0px; +} +.tsd-kind-variable.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -0px; +} +.tsd-kind-variable.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -0px; +} +.tsd-kind-variable.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -0px; +} +.tsd-kind-variable.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -0px; +} +.tsd-kind-variable.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -0px; +} +.tsd-kind-variable.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -0px; +} +.tsd-kind-variable.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -0px; +} +.tsd-kind-variable.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -0px; +} +.tsd-kind-variable.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -0px; +} +.tsd-kind-variable.tsd-parent-kind-enum.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -0px; +} +.tsd-kind-variable.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -0px; +} +.tsd-kind-variable.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -0px; +} + +.tsd-kind-property > .tsd-kind-icon:before { + background-position: -136px -0px; +} +.tsd-kind-property.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -0px; +} +.tsd-kind-property.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -0px; +} +.tsd-kind-property.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -0px; +} +.tsd-kind-property.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -0px; +} +.tsd-kind-property.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -0px; +} +.tsd-kind-property.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -0px; +} +.tsd-kind-property.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -0px; +} +.tsd-kind-property.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -0px; +} +.tsd-kind-property.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -0px; +} +.tsd-kind-property.tsd-parent-kind-enum.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -0px; +} +.tsd-kind-property.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -0px; +} +.tsd-kind-property.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -0px; +} + +.tsd-kind-get-signature > .tsd-kind-icon:before { + background-position: -136px -17px; +} +.tsd-kind-get-signature.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -17px; +} +.tsd-kind-get-signature.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-enum.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -17px; +} +.tsd-kind-get-signature.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -17px; +} + +.tsd-kind-set-signature > .tsd-kind-icon:before { + background-position: -136px -34px; +} +.tsd-kind-set-signature.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -34px; +} +.tsd-kind-set-signature.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-enum.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -34px; +} +.tsd-kind-set-signature.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -34px; +} + +.tsd-kind-accessor > .tsd-kind-icon:before { + background-position: -136px -51px; +} +.tsd-kind-accessor.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -51px; +} +.tsd-kind-accessor.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-enum.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -51px; +} +.tsd-kind-accessor.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -51px; +} + +.tsd-kind-function > .tsd-kind-icon:before { + background-position: -136px -68px; +} +.tsd-kind-function.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -68px; +} +.tsd-kind-function.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-function.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -68px; +} +.tsd-kind-function.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -68px; +} +.tsd-kind-function.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -68px; +} +.tsd-kind-function.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -68px; +} +.tsd-kind-function.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-function.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -68px; +} +.tsd-kind-function.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -68px; +} +.tsd-kind-function.tsd-parent-kind-enum.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-function.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -68px; +} +.tsd-kind-function.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -68px; +} + +.tsd-kind-method > .tsd-kind-icon:before { + background-position: -136px -68px; +} +.tsd-kind-method.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -68px; +} +.tsd-kind-method.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-method.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -68px; +} +.tsd-kind-method.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -68px; +} +.tsd-kind-method.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -68px; +} +.tsd-kind-method.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -68px; +} +.tsd-kind-method.tsd-parent-kind-class.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-method.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -68px; +} +.tsd-kind-method.tsd-parent-kind-enum.tsd-is-protected > .tsd-kind-icon:before { + background-position: -187px -68px; +} +.tsd-kind-method.tsd-parent-kind-enum.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-method.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -68px; +} +.tsd-kind-method.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -68px; +} + +.tsd-kind-call-signature > .tsd-kind-icon:before { + background-position: -136px -68px; +} +.tsd-kind-call-signature.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -68px; +} +.tsd-kind-call-signature.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-enum > .tsd-kind-icon:before { + background-position: -170px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-enum.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-interface > .tsd-kind-icon:before { + background-position: -204px -68px; +} +.tsd-kind-call-signature.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -68px; +} + +.tsd-kind-function.tsd-has-type-parameter > .tsd-kind-icon:before { + background-position: -136px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -153px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-class + > .tsd-kind-icon:before { + background-position: -51px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-enum + > .tsd-kind-icon:before { + background-position: -170px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-enum.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-interface + > .tsd-kind-icon:before { + background-position: -204px -85px; +} +.tsd-kind-function.tsd-has-type-parameter.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -85px; +} + +.tsd-kind-method.tsd-has-type-parameter > .tsd-kind-icon:before { + background-position: -136px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -153px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-class + > .tsd-kind-icon:before { + background-position: -51px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-class.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-enum + > .tsd-kind-icon:before { + background-position: -170px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-enum.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -187px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-enum.tsd-is-private + > .tsd-kind-icon:before { + background-position: -119px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-interface + > .tsd-kind-icon:before { + background-position: -204px -85px; +} +.tsd-kind-method.tsd-has-type-parameter.tsd-parent-kind-interface.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -221px -85px; +} + +.tsd-kind-constructor > .tsd-kind-icon:before { + background-position: -136px -102px; +} +.tsd-kind-constructor.tsd-is-protected > .tsd-kind-icon:before { + background-position: -153px -102px; +} +.tsd-kind-constructor.tsd-is-private > .tsd-kind-icon:before { + background-position: -119px -102px; +} +.tsd-kind-constructor.tsd-parent-kind-class > .tsd-kind-icon:before { + background-position: -51px -102px; +} +.tsd-kind-constructor.tsd-parent-kind-class.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -68px -102px; +} +.tsd-kind-constructor.tsd-parent-kind-class.tsd-is-protected + > .tsd-kind-icon:before { + background-position: -85px -102px; +} +.tsd-kind-constructor.tsd-parent-kind-class.tsd-is-protected.tsd-is-inherited + > .tsd-kind-icon:before { + background-position: -102px -102px; +} 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--color-toolbar: var(--dark-color-toolbar); + --color-toolbar-text: var(--dark-color-toolbar-text); + --icon-filter: var(--dark-icon-filter); + --external-icon: var(--dark-external-icon); + } +} + +body { + margin: 0; +} + +body.light { + --color-background: var(--light-color-background); + --color-secondary-background: var(--light-color-secondary-background); + --color-text: var(--light-color-text); + --color-text-aside: var(--light-color-text-aside); + --color-link: var(--light-color-link); + --color-menu-divider: var(--light-color-menu-divider); + --color-menu-divider-focus: var(--light-color-menu-divider-focus); + --color-menu-label: var(--light-color-menu-label); + --color-panel: var(--light-color-panel); + --color-panel-divider: var(--light-color-panel-divider); + --color-comment-tag: var(--light-color-comment-tag); + --color-comment-tag-text: var(--light-color-comment-tag-text); + --color-ts: var(--light-color-ts); + --color-ts-interface: var(--light-color-ts-interface); + 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var(--dark-color-comment-tag-text); + --color-ts: var(--dark-color-ts); + --color-ts-interface: var(--dark-color-ts-interface); + --color-ts-enum: var(--dark-color-ts-enum); + --color-ts-class: var(--dark-color-ts-class); + --color-ts-private: var(--dark-color-ts-private); + --color-toolbar: var(--dark-color-toolbar); + --color-toolbar-text: var(--dark-color-toolbar-text); + --icon-filter: var(--dark-icon-filter); + --external-icon: var(--dark-external-icon); +} + +h1 { + font-size: 2em; + margin: 0.67em 0; +} + +h2 { + font-size: 1.5em; + margin: 0.83em 0; +} + +h3 { + font-size: 1.17em; + margin: 1em 0; +} + +h4, +.tsd-index-panel h3 { + font-size: 1em; + margin: 1.33em 0; +} + +h5 { + font-size: 0.83em; + margin: 1.67em 0; +} + +h6 { + font-size: 0.67em; + margin: 2.33em 0; +} + +pre { + white-space: pre; + white-space: pre-wrap; + word-wrap: break-word; +} + +dl, +menu, +ol, +ul { + margin: 1em 0; +} + +dd { + margin: 0 0 0 40px; +} + +.container { + max-width: 1200px; + margin: 0 auto; + padding: 0 40px; +} +@media (max-width: 640px) { + .container { + padding: 0 20px; + } +} + +.container-main { + padding-bottom: 200px; +} + +.row { + display: flex; + position: relative; + margin: 0 -10px; +} +.row:after { + visibility: hidden; + display: block; + content: ""; + clear: both; + height: 0; +} + +.col-4, +.col-8 { + box-sizing: border-box; + float: left; + padding: 0 10px; +} + +.col-4 { + width: 33.3333333333%; +} +.col-8 { + width: 66.6666666667%; +} + +ul.tsd-descriptions > li > :first-child, +.tsd-panel > :first-child, +.col-8 > :first-child, +.col-4 > :first-child, +ul.tsd-descriptions > li > :first-child > :first-child, +.tsd-panel > :first-child > :first-child, +.col-8 > :first-child > :first-child, +.col-4 > :first-child > :first-child, +ul.tsd-descriptions > li > :first-child > :first-child > :first-child, +.tsd-panel > :first-child > :first-child > :first-child, +.col-8 > :first-child > :first-child > :first-child, +.col-4 > :first-child > :first-child > :first-child { + margin-top: 0; +} +ul.tsd-descriptions > li > :last-child, +.tsd-panel > :last-child, +.col-8 > :last-child, +.col-4 > :last-child, +ul.tsd-descriptions > li > :last-child > :last-child, +.tsd-panel > :last-child > :last-child, +.col-8 > :last-child > :last-child, +.col-4 > :last-child > :last-child, +ul.tsd-descriptions > li > :last-child > :last-child > :last-child, +.tsd-panel > :last-child > :last-child > :last-child, +.col-8 > :last-child > :last-child > :last-child, +.col-4 > :last-child > :last-child > :last-child { + margin-bottom: 0; +} + +@keyframes fade-in { + from { + opacity: 0; + } + to { + opacity: 1; + } +} +@keyframes fade-out { + from { + opacity: 1; + visibility: visible; + } + to { + opacity: 0; + } +} +@keyframes fade-in-delayed { + 0% { + opacity: 0; + } + 33% { + opacity: 0; + } + 100% { + opacity: 1; + } +} +@keyframes fade-out-delayed { + 0% { + opacity: 1; + visibility: visible; + } + 66% { + opacity: 0; + } + 100% { + opacity: 0; + } +} +@keyframes shift-to-left { + from { + transform: translate(0, 0); + } + to { + transform: translate(-25%, 0); + } +} +@keyframes unshift-to-left { + from { + transform: translate(-25%, 0); + } + to { + transform: translate(0, 0); + } +} +@keyframes pop-in-from-right { + from { + transform: translate(100%, 0); + } + to { + transform: translate(0, 0); + } +} +@keyframes pop-out-to-right { + from { + transform: translate(0, 0); + visibility: visible; + } + to { + transform: translate(100%, 0); + } +} +body { + background: var(--color-background); + font-family: "Segoe UI", sans-serif; + font-size: 16px; + color: var(--color-text); +} + +a { + color: var(--color-link); + text-decoration: none; +} +a:hover { + text-decoration: underline; +} +a.external[target="_blank"] { + background-image: var(--external-icon); + background-position: top 3px right; + background-repeat: no-repeat; + padding-right: 13px; +} + +code, +pre { + font-family: Menlo, Monaco, Consolas, "Courier New", monospace; + padding: 0.2em; + margin: 0; + font-size: 14px; +} + +pre { + padding: 10px; +} +pre code { + padding: 0; + font-size: 100%; +} + +blockquote { + margin: 1em 0; + padding-left: 1em; + border-left: 4px solid gray; +} + +.tsd-typography { + line-height: 1.333em; +} +.tsd-typography ul { + list-style: square; + padding: 0 0 0 20px; + margin: 0; +} +.tsd-typography h4, +.tsd-typography .tsd-index-panel h3, +.tsd-index-panel .tsd-typography h3, +.tsd-typography h5, +.tsd-typography h6 { + font-size: 1em; + margin: 0; +} +.tsd-typography h5, +.tsd-typography h6 { + font-weight: normal; +} +.tsd-typography p, +.tsd-typography ul, +.tsd-typography ol { + margin: 1em 0; +} + +@media (min-width: 901px) and (max-width: 1024px) { + html .col-content { + width: 72%; + } + html .col-menu { + width: 28%; + } + html .tsd-navigation { + padding-left: 10px; + } +} +@media (max-width: 900px) { + html .col-content { + float: none; + width: 100%; + } + html .col-menu { + position: fixed !important; + overflow: auto; + -webkit-overflow-scrolling: touch; + z-index: 1024; + top: 0 !important; + bottom: 0 !important; + left: auto !important; + right: 0 !important; + width: 100%; + padding: 20px 20px 0 0; + max-width: 450px; + visibility: hidden; + background-color: var(--color-panel); + transform: translate(100%, 0); + } + html .col-menu > *:last-child { + padding-bottom: 20px; + } + html .overlay { + content: ""; + display: block; + position: fixed; + z-index: 1023; + top: 0; + left: 0; + right: 0; + bottom: 0; + background-color: rgba(0, 0, 0, 0.75); + visibility: hidden; + } + + .to-has-menu .overlay { + animation: fade-in 0.4s; + } + + .to-has-menu :is(header, footer, .col-content) { + animation: shift-to-left 0.4s; + } + + .to-has-menu .col-menu { + animation: pop-in-from-right 0.4s; + } + + .from-has-menu .overlay { + animation: fade-out 0.4s; + } + + .from-has-menu :is(header, footer, .col-content) { + animation: unshift-to-left 0.4s; + } + + .from-has-menu .col-menu { + animation: pop-out-to-right 0.4s; + } + + .has-menu body { + overflow: hidden; + } + .has-menu .overlay { + visibility: visible; + } + .has-menu :is(header, footer, .col-content) { + transform: translate(-25%, 0); + } + .has-menu .col-menu { + visibility: visible; + transform: translate(0, 0); + display: grid; + grid-template-rows: auto 1fr; + max-height: 100vh; + } + .has-menu .tsd-navigation { + max-height: 100%; + } +} + +.tsd-page-title { + padding: 70px 0 20px 0; + margin: 0 0 40px 0; + background: var(--color-panel); + box-shadow: 0 0 5px rgba(0, 0, 0, 0.35); +} +.tsd-page-title h1 { + margin: 0; +} + +.tsd-breadcrumb { + margin: 0; + padding: 0; + color: var(--color-text-aside); +} +.tsd-breadcrumb a { + color: var(--color-text-aside); + text-decoration: none; +} +.tsd-breadcrumb a:hover { + text-decoration: underline; +} +.tsd-breadcrumb li { + display: inline; +} +.tsd-breadcrumb li:after { + content: " / "; +} + +dl.tsd-comment-tags { + overflow: hidden; +} +dl.tsd-comment-tags dt { + float: left; + padding: 1px 5px; + margin: 0 10px 0 0; + border-radius: 4px; + border: 1px solid var(--color-comment-tag); + color: var(--color-comment-tag); + font-size: 0.8em; + font-weight: normal; +} +dl.tsd-comment-tags dd { + margin: 0 0 10px 0; +} +dl.tsd-comment-tags dd:before, +dl.tsd-comment-tags dd:after { + display: table; + content: " "; +} +dl.tsd-comment-tags dd pre, +dl.tsd-comment-tags dd:after { + clear: both; +} +dl.tsd-comment-tags p { + margin: 0; +} + +.tsd-panel.tsd-comment .lead { + font-size: 1.1em; + line-height: 1.333em; + margin-bottom: 2em; +} +.tsd-panel.tsd-comment .lead:last-child { + margin-bottom: 0; +} + +.toggle-protected .tsd-is-private { + display: none; +} + +.toggle-public .tsd-is-private, +.toggle-public .tsd-is-protected, +.toggle-public .tsd-is-private-protected { + display: none; +} + +.toggle-inherited .tsd-is-inherited { + display: none; +} + +.toggle-externals .tsd-is-external { + display: none; +} + +#tsd-filter { + position: relative; + display: inline-block; + height: 40px; + vertical-align: bottom; +} +.no-filter #tsd-filter { + display: none; +} +#tsd-filter .tsd-filter-group { + display: inline-block; + height: 40px; + vertical-align: bottom; + white-space: nowrap; +} +#tsd-filter input { + display: none; +} +@media (max-width: 900px) { + #tsd-filter .tsd-filter-group { + display: block; + position: absolute; + top: 40px; + right: 20px; + height: auto; + background-color: var(--color-panel); + visibility: hidden; + transform: translate(50%, 0); + box-shadow: 0 0 4px rgba(0, 0, 0, 0.25); + } + .has-options #tsd-filter .tsd-filter-group { + visibility: visible; + } + .to-has-options #tsd-filter .tsd-filter-group { + animation: fade-in 0.2s; + } + .from-has-options #tsd-filter .tsd-filter-group { + animation: fade-out 0.2s; + } + #tsd-filter label, + #tsd-filter .tsd-select { + display: block; + padding-right: 20px; + } +} + +footer { + border-top: 1px solid var(--color-panel-divider); + background-color: var(--color-panel); +} +footer:after { + content: ""; + display: table; +} +footer.with-border-bottom { + border-bottom: 1px solid var(--color-panel-divider); +} +footer .tsd-legend-group { + font-size: 0; +} +footer .tsd-legend { + display: inline-block; + width: 25%; + padding: 0; + font-size: 16px; + list-style: none; + line-height: 1.333em; + vertical-align: top; +} +@media (max-width: 900px) { + footer .tsd-legend { + width: 50%; + } +} + +.tsd-hierarchy { + list-style: square; + padding: 0 0 0 20px; + margin: 0; +} +.tsd-hierarchy .target { + font-weight: bold; +} + +.tsd-index-panel .tsd-index-content { + margin-bottom: -30px !important; +} +.tsd-index-panel .tsd-index-section { + margin-bottom: 30px !important; +} +.tsd-index-panel h3 { + margin: 0 -20px 10px -20px; + padding: 0 20px 10px 20px; + border-bottom: 1px solid var(--color-panel-divider); +} +.tsd-index-panel ul.tsd-index-list { + -webkit-column-count: 3; + -moz-column-count: 3; + -ms-column-count: 3; + -o-column-count: 3; + column-count: 3; + -webkit-column-gap: 20px; + -moz-column-gap: 20px; + -ms-column-gap: 20px; + -o-column-gap: 20px; + column-gap: 20px; + padding: 0; + list-style: none; + line-height: 1.333em; +} +@media (max-width: 900px) { + .tsd-index-panel ul.tsd-index-list { + -webkit-column-count: 1; + -moz-column-count: 1; + -ms-column-count: 1; + -o-column-count: 1; + column-count: 1; + } +} +@media (min-width: 901px) and (max-width: 1024px) { + .tsd-index-panel ul.tsd-index-list { + -webkit-column-count: 2; + -moz-column-count: 2; + -ms-column-count: 2; + -o-column-count: 2; + column-count: 2; + } +} +.tsd-index-panel ul.tsd-index-list li { + -webkit-page-break-inside: avoid; + -moz-page-break-inside: avoid; + -ms-page-break-inside: avoid; + -o-page-break-inside: avoid; + page-break-inside: avoid; +} +.tsd-index-panel a, +.tsd-index-panel .tsd-parent-kind-module a { + color: var(--color-ts); +} +.tsd-index-panel .tsd-parent-kind-interface a { + color: var(--color-ts-interface); +} +.tsd-index-panel .tsd-parent-kind-enum a { + color: var(--color-ts-enum); +} +.tsd-index-panel .tsd-parent-kind-class a { + color: var(--color-ts-class); +} +.tsd-index-panel .tsd-kind-module a { + color: var(--color-ts); +} +.tsd-index-panel .tsd-kind-interface a { + color: var(--color-ts-interface); +} +.tsd-index-panel .tsd-kind-enum a { + color: var(--color-ts-enum); +} +.tsd-index-panel .tsd-kind-class a { + color: var(--color-ts-class); +} +.tsd-index-panel .tsd-is-private a { + color: var(--color-ts-private); +} + +.tsd-flag { + display: inline-block; + padding: 1px 5px; + border-radius: 4px; + color: var(--color-comment-tag-text); + background-color: var(--color-comment-tag); + text-indent: 0; + font-size: 14px; + font-weight: normal; +} + +.tsd-anchor { + position: absolute; + top: -100px; +} + +.tsd-member { + position: relative; +} +.tsd-member .tsd-anchor + h3 { + margin-top: 0; + margin-bottom: 0; + border-bottom: none; +} +.tsd-member [data-tsd-kind] { + color: var(--color-ts); +} +.tsd-member [data-tsd-kind="Interface"] { + color: var(--color-ts-interface); +} +.tsd-member [data-tsd-kind="Enum"] { + color: var(--color-ts-enum); +} +.tsd-member [data-tsd-kind="Class"] { + color: var(--color-ts-class); +} +.tsd-member [data-tsd-kind="Private"] { + color: var(--color-ts-private); +} + +.tsd-navigation { + margin: 0 0 0 40px; +} +.tsd-navigation a { + display: block; + padding-top: 2px; + padding-bottom: 2px; + border-left: 2px solid transparent; + color: var(--color-text); + text-decoration: none; + transition: border-left-color 0.1s; +} +.tsd-navigation a:hover { + text-decoration: underline; +} +.tsd-navigation ul { + margin: 0; + padding: 0; + list-style: none; +} +.tsd-navigation li { + padding: 0; +} + +.tsd-navigation.primary { + padding-bottom: 40px; +} +.tsd-navigation.primary a { + display: block; + padding-top: 6px; + padding-bottom: 6px; +} +.tsd-navigation.primary ul li a { + padding-left: 5px; +} +.tsd-navigation.primary ul li li a { + padding-left: 25px; +} +.tsd-navigation.primary ul li li li a { + padding-left: 45px; +} +.tsd-navigation.primary ul li li li li a { + padding-left: 65px; +} +.tsd-navigation.primary ul li li li li li a { + padding-left: 85px; +} +.tsd-navigation.primary ul li li li li li li a { + padding-left: 105px; +} +.tsd-navigation.primary > ul { + border-bottom: 1px solid var(--color-panel-divider); +} +.tsd-navigation.primary li { + border-top: 1px solid var(--color-panel-divider); +} +.tsd-navigation.primary li.current > a { + font-weight: bold; +} +.tsd-navigation.primary li.label span { + display: block; + padding: 20px 0 6px 5px; + color: var(--color-menu-label); +} +.tsd-navigation.primary li.globals + li > span, +.tsd-navigation.primary li.globals + li > a { + padding-top: 20px; +} + +.tsd-navigation.secondary { + max-height: calc(100vh - 1rem - 40px); + overflow: auto; + position: sticky; + top: calc(0.5rem + 40px); + transition: 0.3s; +} +.tsd-navigation.secondary.tsd-navigation--toolbar-hide { + max-height: calc(100vh - 1rem); + top: 0.5rem; +} +.tsd-navigation.secondary ul { + transition: opacity 0.2s; +} +.tsd-navigation.secondary ul li a { + padding-left: 25px; +} +.tsd-navigation.secondary ul li li a { + padding-left: 45px; +} +.tsd-navigation.secondary ul li li li a { + padding-left: 65px; +} +.tsd-navigation.secondary ul li li li li a { + padding-left: 85px; +} +.tsd-navigation.secondary ul li li li li li a { + padding-left: 105px; +} +.tsd-navigation.secondary ul li li li li li li a { + padding-left: 125px; +} +.tsd-navigation.secondary ul.current a { + border-left-color: var(--color-panel-divider); +} +.tsd-navigation.secondary li.focus > a, +.tsd-navigation.secondary ul.current li.focus > a { + border-left-color: var(--color-menu-divider-focus); +} +.tsd-navigation.secondary li.current { + margin-top: 20px; + margin-bottom: 20px; + border-left-color: var(--color-panel-divider); +} +.tsd-navigation.secondary li.current > a { + font-weight: bold; +} + +@media (min-width: 901px) { + .menu-sticky-wrap { + position: static; + } +} + +.tsd-panel { + margin: 20px 0; + padding: 20px; + background-color: var(--color-panel); + box-shadow: 0 0 4px rgba(0, 0, 0, 0.25); +} +.tsd-panel:empty { + display: none; +} +.tsd-panel > h1, +.tsd-panel > h2, +.tsd-panel > h3 { + margin: 1.5em -20px 10px -20px; + padding: 0 20px 10px 20px; + border-bottom: 1px solid var(--color-panel-divider); +} +.tsd-panel > h1.tsd-before-signature, +.tsd-panel > h2.tsd-before-signature, +.tsd-panel > h3.tsd-before-signature { + margin-bottom: 0; + border-bottom: 0; +} +.tsd-panel table { + display: block; + width: 100%; + overflow: auto; + margin-top: 10px; + word-break: normal; + word-break: keep-all; + border-collapse: collapse; +} +.tsd-panel table th { + font-weight: bold; +} +.tsd-panel table th, +.tsd-panel table td { + padding: 6px 13px; + border: 1px solid var(--color-panel-divider); +} +.tsd-panel table tr { + background: var(--color-background); +} +.tsd-panel table tr:nth-child(even) { + background: var(--color-secondary-background); +} + +.tsd-panel-group { + margin: 60px 0; +} +.tsd-panel-group > h1, +.tsd-panel-group > h2, +.tsd-panel-group > h3 { + padding-left: 20px; + padding-right: 20px; +} + +#tsd-search { + transition: background-color 0.2s; +} +#tsd-search .title { + position: relative; + z-index: 2; +} +#tsd-search .field { + position: absolute; + left: 0; + top: 0; + right: 40px; + height: 40px; +} +#tsd-search .field input { + box-sizing: border-box; + position: relative; + top: -50px; + z-index: 1; + width: 100%; + padding: 0 10px; + opacity: 0; + outline: 0; + border: 0; + background: transparent; + color: var(--color-text); +} +#tsd-search .field label { + position: absolute; + overflow: hidden; + right: -40px; +} +#tsd-search .field input, +#tsd-search .title { + transition: opacity 0.2s; +} +#tsd-search .results { + position: absolute; + visibility: hidden; + top: 40px; + width: 100%; + margin: 0; + padding: 0; + list-style: none; + box-shadow: 0 0 4px rgba(0, 0, 0, 0.25); +} +#tsd-search .results li { + padding: 0 10px; + background-color: var(--color-background); +} +#tsd-search .results li:nth-child(even) { + background-color: var(--color-panel); +} +#tsd-search .results li.state { + display: none; +} +#tsd-search .results li.current, +#tsd-search .results li:hover { + background-color: var(--color-panel-divider); +} +#tsd-search .results a { + display: block; +} +#tsd-search .results a:before { + top: 10px; +} +#tsd-search .results span.parent { + color: var(--color-text-aside); + font-weight: normal; +} +#tsd-search.has-focus { + background-color: var(--color-panel-divider); +} +#tsd-search.has-focus .field input { + top: 0; + opacity: 1; +} +#tsd-search.has-focus .title { + z-index: 0; + opacity: 0; +} +#tsd-search.has-focus .results { + visibility: visible; +} +#tsd-search.loading .results li.state.loading { + display: block; +} +#tsd-search.failure .results li.state.failure { + display: block; +} + +.tsd-signature { + margin: 0 0 1em 0; + padding: 10px; + border: 1px solid var(--color-panel-divider); + font-family: Menlo, Monaco, Consolas, "Courier New", monospace; + font-size: 14px; + overflow-x: auto; +} +.tsd-signature.tsd-kind-icon { + padding-left: 30px; +} +.tsd-signature.tsd-kind-icon:before { + top: 10px; + left: 10px; +} +.tsd-panel > .tsd-signature { + margin-left: -20px; + margin-right: -20px; + border-width: 1px 0; +} +.tsd-panel > .tsd-signature.tsd-kind-icon { + padding-left: 40px; +} +.tsd-panel > .tsd-signature.tsd-kind-icon:before { + left: 20px; +} + +.tsd-signature-symbol { + color: var(--color-text-aside); + font-weight: normal; +} + +.tsd-signature-type { + font-style: italic; + font-weight: normal; +} + +.tsd-signatures { + padding: 0; + margin: 0 0 1em 0; + border: 1px solid var(--color-panel-divider); +} +.tsd-signatures .tsd-signature { + margin: 0; + border-width: 1px 0 0 0; + transition: background-color 0.1s; +} +.tsd-signatures .tsd-signature:first-child { + border-top-width: 0; +} +.tsd-signatures .tsd-signature.current { + background-color: var(--color-panel-divider); +} +.tsd-signatures.active > .tsd-signature { + cursor: pointer; +} +.tsd-panel > .tsd-signatures { + margin-left: -20px; + margin-right: -20px; + border-width: 1px 0; +} +.tsd-panel > .tsd-signatures .tsd-signature.tsd-kind-icon { + padding-left: 40px; +} +.tsd-panel > .tsd-signatures .tsd-signature.tsd-kind-icon:before { + left: 20px; +} +.tsd-panel > a.anchor + .tsd-signatures { + border-top-width: 0; + margin-top: -20px; +} + +ul.tsd-descriptions { + position: relative; + overflow: hidden; + padding: 0; + list-style: none; +} +ul.tsd-descriptions.active > .tsd-description { + display: none; +} +ul.tsd-descriptions.active > .tsd-description.current { + display: block; +} +ul.tsd-descriptions.active > .tsd-description.fade-in { + animation: fade-in-delayed 0.3s; +} +ul.tsd-descriptions.active > .tsd-description.fade-out { + animation: fade-out-delayed 0.3s; + position: absolute; + display: block; + top: 0; + left: 0; + right: 0; + opacity: 0; + visibility: hidden; +} +ul.tsd-descriptions h4, +ul.tsd-descriptions .tsd-index-panel h3, +.tsd-index-panel ul.tsd-descriptions h3 { + font-size: 16px; + margin: 1em 0 0.5em 0; +} + +ul.tsd-parameters, +ul.tsd-type-parameters { + list-style: square; + margin: 0; + padding-left: 20px; +} +ul.tsd-parameters > li.tsd-parameter-signature, +ul.tsd-type-parameters > li.tsd-parameter-signature { + list-style: none; + margin-left: -20px; +} +ul.tsd-parameters h5, +ul.tsd-type-parameters h5 { + font-size: 16px; + margin: 1em 0 0.5em 0; +} +ul.tsd-parameters .tsd-comment, +ul.tsd-type-parameters .tsd-comment { + margin-top: -0.5em; +} + +.tsd-sources { + font-size: 14px; + color: var(--color-text-aside); + margin: 0 0 1em 0; +} +.tsd-sources a { + color: var(--color-text-aside); + text-decoration: underline; +} +.tsd-sources ul, +.tsd-sources p { + margin: 0 !important; +} +.tsd-sources ul { + list-style: none; + padding: 0; +} + +.tsd-page-toolbar { + position: fixed; + z-index: 1; + top: 0; + left: 0; + width: 100%; + height: 40px; + color: var(--color-toolbar-text); + background: var(--color-toolbar); + border-bottom: 1px solid var(--color-panel-divider); + transition: transform 0.3s linear; +} +.tsd-page-toolbar a { + color: var(--color-toolbar-text); + text-decoration: none; +} +.tsd-page-toolbar a.title { + font-weight: bold; +} +.tsd-page-toolbar a.title:hover { + text-decoration: underline; +} +.tsd-page-toolbar .table-wrap { + display: table; + width: 100%; + height: 40px; +} +.tsd-page-toolbar .table-cell { + display: table-cell; + position: relative; + white-space: nowrap; + line-height: 40px; +} +.tsd-page-toolbar .table-cell:first-child { + width: 100%; +} + +.tsd-page-toolbar--hide { + transform: translateY(-100%); +} + +.tsd-select .tsd-select-list li:before, +.tsd-select .tsd-select-label:before, +.tsd-widget:before { + content: ""; + display: inline-block; + width: 40px; + height: 40px; + margin: 0 -8px 0 0; + background-image: url(./widgets.png); + background-repeat: no-repeat; + text-indent: -1024px; + vertical-align: bottom; + filter: var(--icon-filter); +} +@media (-webkit-min-device-pixel-ratio: 1.5), (min-resolution: 144dpi) { + .tsd-select .tsd-select-list li:before, + .tsd-select .tsd-select-label:before, + .tsd-widget:before { + background-image: url(./widgets@2x.png); + background-size: 320px 40px; + } +} + +.tsd-widget { + display: inline-block; + overflow: hidden; + opacity: 0.8; + height: 40px; + transition: opacity 0.1s, background-color 0.2s; + vertical-align: bottom; + cursor: pointer; +} +.tsd-widget:hover { + opacity: 0.9; +} +.tsd-widget.active { + opacity: 1; + background-color: var(--color-panel-divider); +} +.tsd-widget.no-caption { + width: 40px; +} +.tsd-widget.no-caption:before { + margin: 0; +} +.tsd-widget.search:before { + background-position: 0 0; +} +.tsd-widget.menu:before { + background-position: -40px 0; +} +.tsd-widget.options:before { + background-position: -80px 0; +} +.tsd-widget.options, +.tsd-widget.menu { + display: none; +} +@media (max-width: 900px) { + .tsd-widget.options, + .tsd-widget.menu { + display: inline-block; + } +} +input[type="checkbox"] + .tsd-widget:before { + background-position: -120px 0; +} +input[type="checkbox"]:checked + .tsd-widget:before { + background-position: -160px 0; +} + +.tsd-select { + position: relative; + display: inline-block; + height: 40px; + transition: opacity 0.1s, background-color 0.2s; + vertical-align: bottom; + cursor: pointer; +} +.tsd-select .tsd-select-label { + opacity: 0.6; + transition: opacity 0.2s; +} +.tsd-select .tsd-select-label:before { + background-position: -240px 0; +} +.tsd-select.active .tsd-select-label { + opacity: 0.8; +} +.tsd-select.active .tsd-select-list { + visibility: visible; + opacity: 1; + transition-delay: 0s; +} +.tsd-select .tsd-select-list { + position: absolute; + visibility: hidden; + top: 40px; + left: 0; + margin: 0; + padding: 0; + opacity: 0; + list-style: none; + box-shadow: 0 0 4px rgba(0, 0, 0, 0.25); + transition: visibility 0s 0.2s, opacity 0.2s; +} +.tsd-select .tsd-select-list li { + padding: 0 20px 0 0; + background-color: var(--color-background); +} +.tsd-select .tsd-select-list li:before { + background-position: 40px 0; +} +.tsd-select .tsd-select-list li:nth-child(even) { + background-color: var(--color-panel); +} +.tsd-select .tsd-select-list li:hover { + background-color: var(--color-panel-divider); +} +.tsd-select .tsd-select-list li.selected:before { + background-position: -200px 0; +} +@media (max-width: 900px) { + .tsd-select .tsd-select-list { + top: 0; + left: auto; + right: 100%; + margin-right: -5px; + } + .tsd-select .tsd-select-label:before { + background-position: -280px 0; + } +} + +img { + max-width: 100%; +} diff --git a/docs/assets/widgets.png 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Class ArraySchema

+

Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema

+

Hierarchy

  • Saveable
    • ArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | RecordSchema | EnumSchema | ArraySchema | (string | RecordSchema | EnumSchema | ArraySchema)[]
+

Defines the type of the array elements.

+

loadingOptions

loadingOptions: LoadingOptions

type

type: ARRAY
+

Must be array

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/docs/classes/CommandInputArraySchema.html b/docs/classes/CommandInputArraySchema.html new file mode 100644 index 0000000..65398f6 --- /dev/null +++ b/docs/classes/CommandInputArraySchema.html @@ -0,0 +1,28 @@ +CommandInputArraySchema | cwl-ts-auto
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Class CommandInputArraySchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema

+

Hierarchy

  • Saveable
    • CommandInputArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

items

items: string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | (string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

Legend

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  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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Generated using TypeDoc

\ No newline at end of file diff --git a/docs/classes/CommandInputEnumSchema.html b/docs/classes/CommandInputEnumSchema.html new file mode 100644 index 0000000..7fe240d --- /dev/null +++ b/docs/classes/CommandInputEnumSchema.html @@ -0,0 +1,28 @@ +CommandInputEnumSchema | cwl-ts-auto
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Class CommandInputEnumSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema

+

Hierarchy

  • Saveable
    • CommandInputEnumSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

Legend

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  • Static property
  • Static method
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\ No newline at end of file diff --git a/docs/classes/CommandInputParameter.html b/docs/classes/CommandInputParameter.html new file mode 100644 index 0000000..6660c80 --- /dev/null +++ b/docs/classes/CommandInputParameter.html @@ -0,0 +1,102 @@ +CommandInputParameter | cwl-ts-auto
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Class CommandInputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputParameter

+

An input parameter for a CommandLineTool.

+

Hierarchy

  • Saveable
    • CommandInputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turns the input parameters of a process into +command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | (string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
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  • Inherited property

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\ No newline at end of file diff --git a/docs/classes/CommandInputRecordField.html b/docs/classes/CommandInputRecordField.html new file mode 100644 index 0000000..cb40acd --- /dev/null +++ b/docs/classes/CommandInputRecordField.html @@ -0,0 +1,95 @@ +CommandInputRecordField | cwl-ts-auto
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Class CommandInputRecordField

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField

+

Hierarchy

  • Saveable
    • CommandInputRecordField

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

name

name: string
+

The name of the field

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | (string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

The field type

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/CommandInputRecordSchema.html b/docs/classes/CommandInputRecordSchema.html new file mode 100644 index 0000000..5eed66d --- /dev/null +++ b/docs/classes/CommandInputRecordSchema.html @@ -0,0 +1,28 @@ +CommandInputRecordSchema | cwl-ts-auto
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Class CommandInputRecordSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordSchema

+

Hierarchy

  • Saveable
    • CommandInputRecordSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: CommandInputRecordField[]
+

Defines the fields of the record.

+

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/CommandLineBindable.html b/docs/classes/CommandLineBindable.html new file mode 100644 index 0000000..3f6bb31 --- /dev/null +++ b/docs/classes/CommandLineBindable.html @@ -0,0 +1,18 @@ +CommandLineBindable | cwl-ts-auto
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Class CommandLineBindable

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBindable

+

Hierarchy

  • Saveable
    • CommandLineBindable

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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Class CommandLineBinding

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineBinding

+

When listed under inputBinding in the input schema, the term +"value" refers to the the corresponding value in the input object. For +binding objects listed in CommandLineTool.arguments, the term "value" +refers to the effective value after evaluating valueFrom.

+

The binding behavior when building the command line depends on the data +type of the value. If there is a mismatch between the type described by +the input schema and the effective value, such as resulting from an +expression evaluation, an implementation must use the data type of the +effective value.

+
    +

  • string: Add prefix and the string to the command line.

    +
    • +

  • number: Add prefix and decimal representation to command line.

    +
    • +

  • boolean: If true, add prefix to the command line. If false, add + nothing.

    +
    • +

  • File: Add prefix and the value of +File.path to the command line.

    +
    • +

  • Directory: Add prefix and the value of +Directory.path to the command line.

    +
    • +

  • array: If itemSeparator is specified, add prefix and the join + the array into a single string with itemSeparator separating the + items. Otherwise first add prefix, then recursively process + individual elements. + If the array is empty, it does not add anything to command line.

    +
    • +

  • object: Add prefix only, and recursively add object fields for + which inputBinding is specified.

    +
    • +

  • null: Add nothing.

    +
    • +
+

Hierarchy

  • Saveable
    • CommandLineBinding

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional itemSeparator

itemSeparator?: string
+

Join the array elements into a single string with the elements +separated by by itemSeparator.

+

Optional loadContents

loadContents?: boolean
+

Use of loadContents in InputBinding is deprecated. +Preserved for v1.0 backwards compatability. Will be removed in +CWL v2.0. Use InputParameter.loadContents instead.

+

loadingOptions

loadingOptions: LoadingOptions

Optional position

position?: string | number
+

The sorting key. Default position is 0. If a CWL Parameter Reference +or CWL Expression is used and if the +inputBinding is associated with an input parameter, then the value of +self will be the value of the input parameter. Input parameter +defaults (as specified by the InputParameter.default field) must be +applied before evaluating the expression. Expressions must return a +single value of type int or a null.

+

Optional prefix

prefix?: string
+

Command line prefix to add before the value.

+

Optional separate

separate?: boolean
+

If true (default), then the prefix and value must be added as separate +command line arguments; if false, prefix and value must be concatenated +into a single command line argument.

+

Optional shellQuote

shellQuote?: boolean
+

If ShellCommandRequirement is in the requirements for the current command, +this controls whether the value is quoted on the command line (default is true). +Use shellQuote: false to inject metacharacters for operations such as pipes.

+

If shellQuote is true or not provided, the implementation must not +permit interpretation of any shell metacharacters or directives.

+

Optional valueFrom

valueFrom?: string
+

If valueFrom is a constant string value, use this as the value and +apply the binding rules above.

+

If valueFrom is an expression, evaluate the expression to yield the +actual value to use to build the command line and apply the binding +rules above. If the inputBinding is associated with an input +parameter, the value of self in the expression will be the value of +the input parameter. Input parameter defaults (as specified by the +InputParameter.default field) must be applied before evaluating the +expression.

+

If the value of the associated input parameter is null, valueFrom is +not evaluated and nothing is added to the command line.

+

When a binding is part of the CommandLineTool.arguments field, +the valueFrom field is required.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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Class CommandLineTool

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandLineTool

+

This defines the schema of the CWL Command Line Tool Description document.

+

Hierarchy

  • Saveable
    • CommandLineTool

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional arguments_

arguments_?: (string | CommandLineBinding)[]
+

Command line bindings which are not directly associated with input +parameters. If the value is a string, it is used as a string literal +argument. If it is an Expression, the result of the evaluation is used +as an argument.

+

Optional baseCommand

baseCommand?: string | string[]
+

Specifies the program to execute. If an array, the first element of +the array is the command to execute, and subsequent elements are +mandatory command line arguments. The elements in baseCommand must +appear before any command line bindings from inputBinding or +arguments.

+

If baseCommand is not provided or is an empty array, the first +element of the command line produced after processing inputBinding or +arguments must be used as the program to execute.

+

If the program includes a path separator character it must +be an absolute path, otherwise it is an error. If the program does not +include a path separator, search the $PATH variable in the runtime +environment of the workflow runner find the absolute path of the +executable.

+

class_

class_: COMMANDLINETOOL

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: CommandInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: CommandOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional permanentFailCodes

permanentFailCodes?: number[]
+

Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. +If not specified, all exit codes except 0 are considered permanent failure.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

Optional stderr

stderr?: string
+

Capture the command's standard error stream to a file written to +the designated output directory.

+

If stderr is a string, it specifies the file name to use.

+

If stderr is an expression, the expression is evaluated and must +return a string with the file name to use to capture stderr. If the +return value is not a string, or the resulting path contains illegal +characters (such as the path separator /) it is an error.

+

Optional stdin

stdin?: string
+

A path to a file whose contents must be piped into the command's +standard input stream.

+

Optional stdout

stdout?: string
+

Capture the command's standard output stream to a file written to +the designated output directory.

+

If stdout is a string, it specifies the file name to use.

+

If stdout is an expression, the expression is evaluated and must +return a string with the file name to use to capture stdout. If the +return value is not a string, or the resulting path contains illegal +characters (such as the path separator /) it is an error.

+

Optional successCodes

successCodes?: number[]
+

Exit codes that indicate the process completed successfully.

+

If not specified, only exit code 0 is considered success.

+

Optional temporaryFailCodes

temporaryFailCodes?: number[]
+

Exit codes that indicate the process failed due to a possibly +temporary condition, where executing the process with the same +runtime environment and inputs may produce different results.

+

If not specified, no exit codes are considered temporary failure.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/CommandOutputArraySchema.html b/docs/classes/CommandOutputArraySchema.html new file mode 100644 index 0000000..5b7aacc --- /dev/null +++ b/docs/classes/CommandOutputArraySchema.html @@ -0,0 +1,26 @@ +CommandOutputArraySchema | cwl-ts-auto
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Class CommandOutputArraySchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema

+

Hierarchy

  • Saveable
    • CommandOutputArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema | (string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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Class CommandOutputBinding

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputBinding

+

Describes how to generate an output parameter based on the files produced +by a CommandLineTool.

+

The output parameter value is generated by applying these operations in the +following order:

+
    +
  • glob
    • +
  • loadContents
    • +
  • outputEval
    • +
  • secondaryFiles
    • +
+

Hierarchy

  • Saveable
    • CommandOutputBinding

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional glob

glob?: string | string[]
+

Find files or directories relative to the output directory, using POSIX +glob(3) pathname matching. If an array is provided, find files or +directories that match any pattern in the array. If an expression is +provided, the expression must return a string or an array of strings, +which will then be evaluated as one or more glob patterns. Must only +match and return files/directories which actually exist.

+

If the value of glob is a relative path pattern (does not +begin with a slash '/') then it is resolved relative to the +output directory. If the value of the glob is an absolute +path pattern (it does begin with a slash '/') then it must +refer to a path within the output directory. It is an error +if any glob resolves to a path outside the output directory. +Specifically this means globs that resolve to paths outside the output +directory are illegal.

+

A glob may match a path within the output directory which is +actually a symlink to another file. In this case, the +expected behavior is for the resulting File/Directory object to take the +basename (and corresponding nameroot and nameext) of the +symlink. The location of the File/Directory is implementation +dependent, but logically the File/Directory should have the same content +as the symlink target. Platforms may stage output files/directories to +cloud storage that lack the concept of a symlink. In +this case file content and directories may be duplicated, or (to avoid +duplication) the File/Directory location may refer to the symlink +target.

+

It is an error if a symlink in the output directory (or any +symlink in a chain of links) refers to any file or directory +that is not under an input or output directory.

+

Implementations may shut down a container before globbing +output, so globs and expressions must not assume access to the +container filesystem except for declared input and output.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

Optional outputEval

outputEval?: string
+

Evaluate an expression to generate the output value. If +glob was specified, the value of self must be an array +containing file objects that were matched. If no files were +matched, self must be a zero length array; if a single file +was matched, the value of self is an array of a single +element. The exit code of the process is +available in the expression as runtime.exitCode.

+

Additionally if loadContents is true, the file must be a +UTF-8 text file 64 KiB or smaller, and the implementation must +read the entire contents of the file (or file array) and place +it in the contents field of the File object for use in +outputEval. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

If a tool needs to return a large amount of structured data to +the workflow, loading the output object from cwl.output.json +bypasses outputEval and is not subject to the 64 KiB +loadContents limit.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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Class CommandOutputEnumSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema

+

Hierarchy

  • Saveable
    • CommandOutputEnumSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/CommandOutputParameter.html b/docs/classes/CommandOutputParameter.html new file mode 100644 index 0000000..1572dbe --- /dev/null +++ b/docs/classes/CommandOutputParameter.html @@ -0,0 +1,76 @@ +CommandOutputParameter | cwl-ts-auto
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Class CommandOutputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputParameter

+

An output parameter for a CommandLineTool.

+

Hierarchy

  • Saveable
    • CommandOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional outputBinding

outputBinding?: CommandOutputBinding
+

Describes how to generate this output object based on the files produced by a CommandLineTool

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema | (string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/CommandOutputRecordField.html b/docs/classes/CommandOutputRecordField.html new file mode 100644 index 0000000..4d7f3b7 --- /dev/null +++ b/docs/classes/CommandOutputRecordField.html @@ -0,0 +1,76 @@ +CommandOutputRecordField | cwl-ts-auto
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Class CommandOutputRecordField

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField

+

Hierarchy

  • Saveable
    • CommandOutputRecordField

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

name

name: string
+

The name of the field

+

Optional outputBinding

outputBinding?: CommandOutputBinding
+

Describes how to generate this output object based on the files +produced by a CommandLineTool

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema | (string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema)[]
+

The field type

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/CommandOutputRecordSchema.html b/docs/classes/CommandOutputRecordSchema.html new file mode 100644 index 0000000..6cec890 --- /dev/null +++ b/docs/classes/CommandOutputRecordSchema.html @@ -0,0 +1,26 @@ +CommandOutputRecordSchema | cwl-ts-auto
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Class CommandOutputRecordSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema

+

Hierarchy

  • Saveable
    • CommandOutputRecordSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: CommandOutputRecordField[]
+

Defines the fields of the record.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/Directory.html b/docs/classes/Directory.html new file mode 100644 index 0000000..e7461b7 --- /dev/null +++ b/docs/classes/Directory.html @@ -0,0 +1,98 @@ +Directory | cwl-ts-auto
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Class Directory

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#Directory

+

Represents a directory to present to a command line tool.

+

Directories are represented as objects with class of Directory. Directory objects have +a number of properties that provide metadata about the directory.

+

The location property of a Directory is a URI that uniquely identifies +the directory. Implementations must support the file:// URI scheme and may +support other schemes such as http://. Alternately to location, +implementations must also accept the path property on Directory, which +must be a filesystem path available on the same host as the CWL runner (for +inputs) or the runtime environment of a command line tool execution (for +command line tool outputs).

+

A Directory object may have a listing field. This is a list of File and +Directory objects that are contained in the Directory. For each entry in +listing, the basename property defines the name of the File or +Subdirectory when staged to disk. If listing is not provided, the +implementation must have some way of fetching the Directory listing at +runtime based on the location field.

+

If a Directory does not have location, it is a Directory literal. A +Directory literal must provide listing. Directory literals must be +created on disk at runtime as needed.

+

The resources in a Directory literal do not need to have any implied +relationship in their location. For example, a Directory listing may +contain two files located on different hosts. It is the responsibility of +the runtime to ensure that those files are staged to disk appropriately. +Secondary files associated with files in listing must also be staged to +the same Directory.

+

When executing a CommandLineTool, Directories must be recursively staged +first and have local values of path assigend.

+

Directory objects in CommandLineTool output must provide either a +location URI or a path property in the context of the tool execution +runtime (local to the compute node, or within the executing container).

+

An ExpressionTool may forward file references from input to output by using +the same value for location.

+

Name conflicts (the same basename appearing multiple times in listing +or in any entry in secondaryFiles in the listing) is a fatal error.

+

Hierarchy

  • Saveable
    • Directory

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional basename

basename?: string
+

The base name of the directory, that is, the name of the file without any +leading directory path. The base name must not contain a slash /.

+

If not provided, the implementation must set this field based on the +location field by taking the final path component after parsing +location as an IRI. If basename is provided, it is not required to +match the value from location.

+

When this file is made available to a CommandLineTool, it must be named +with basename, i.e. the final component of the path field must match +basename.

+

class_

class_: DIRECTORY
+

Must be Directory to indicate this object describes a Directory.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional listing

listing?: (File | Directory)[]
+

List of files or subdirectories contained in this directory. The name +of each file or subdirectory is determined by the basename field of +each File or Directory object. It is an error if a File shares a +basename with any other entry in listing. If two or more +Directory object share the same basename, this must be treated as +equivalent to a single subdirectory with the listings recursively +merged.

+

loadingOptions

loadingOptions: LoadingOptions

Optional location

location?: string
+

An IRI that identifies the directory resource. This may be a relative +reference, in which case it must be resolved using the base IRI of the +document. The location may refer to a local or remote resource. If +the listing field is not set, the implementation must use the +location IRI to retrieve directory listing. If an implementation is +unable to retrieve the directory listing stored at a remote resource (due to +unsupported protocol, access denied, or other issue) it must signal an +error.

+

If the location field is not provided, the listing field must be +provided. The implementation must assign a unique identifier for +the location field.

+

If the path field is provided but the location field is not, an +implementation may assign the value of the path field to location, +then follow the rules above.

+

Optional path

path?: string
+

The local path where the Directory is made available prior to executing a +CommandLineTool. This must be set by the implementation. This field +must not be used in any other context. The command line tool being +executed must be able to to access the directory at path using the POSIX +opendir(2) syscall.

+

If the path contains POSIX shell metacharacters +(|,&, ;, <, >, (,), $,`, \, ", ', +<space>, <tab>, and <newline>) or characters +not allowed +for Internationalized Domain Names for Applications +then implementations may terminate the process with a +permanentFailure.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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Class Dirent

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#Dirent

+

Define a file or subdirectory that must be staged to a particular +place prior to executing the command line tool. May be the result +of executing an expression, such as building a configuration file +from a template.

+

Usually files are staged within the designated output directory. +However, under certain circumstances, files may be staged at +arbitrary locations, see discussion for entryname.

+

Hierarchy

  • Saveable
    • Dirent

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

entry

entry: string
+

If the value is a string literal or an expression which evaluates to a +string, a new text file must be created with the string as the file contents.

+

If the value is an expression that evaluates to a File or +Directory object, or an array of File or Directory +objects, this indicates the referenced file or directory +should be added to the designated output directory prior to +executing the tool.

+

If the value is an expression that evaluates to null, +nothing is added to the designated output directory, the entry +has no effect.

+

If the value is an expression that evaluates to some other +array, number, or object not consisting of File or +Directory objects, a new file must be created with the value +serialized to JSON text as the file contents. The JSON +serialization behavior should match the behavior of string +interpolation of Parameter +references.

+

Optional entryname

entryname?: string
+

The "target" name of the file or subdirectory. If entry is +a File or Directory, the entryname field overrides the value +of basename of the File or Directory object.

+
    +
  • Required when entry evaluates to file contents only
    • +
  • Optional when entry evaluates to a File or Directory object with a basename
    • +
  • Invalid when entry evaluates to an array of File or Directory objects.
    • +
+

If entryname is a relative path, it specifies a name within +the designated output directory. A relative path starting +with ../ or that resolves to location above the designated output directory is an error.

+

If entryname is an absolute path (starts with a slash /) +it is an error unless the following conditions are met:

+
    +
  • DockerRequirement is present in requirements
    • +
  • The program is will run inside a software container + where, from the perspective of the program, the root + filesystem is not shared with any other user or + running program.
    • +
+

In this case, and the above conditions are met, then +entryname may specify the absolute path within the container +where the file or directory must be placed.

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Optional writable

writable?: boolean
+

If true, the File or Directory (or array of Files or +Directories) declared in entry must be writable by the tool.

+

Changes to the file or directory must be isolated and not +visible by any other CommandLineTool process. This may be +implemented by making a copy of the original file or +directory.

+

Disruptive changes to the referenced file or directory must not +be allowed unless InplaceUpdateRequirement.inplaceUpdate is true.

+

Default false (files and directories read-only by default).

+

A directory marked as writable: true implies that all files and +subdirectories are recursively writable as well.

+

If writable is false, the file may be made available using a +bind mount or file system link to avoid unnecessary copying of +the input file. Command line tools may receive an error on +attempting to rename or delete files or directories that are +not explicitly marked as writable.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/DockerRequirement.html b/docs/classes/DockerRequirement.html new file mode 100644 index 0000000..a7505c7 --- /dev/null +++ b/docs/classes/DockerRequirement.html @@ -0,0 +1,81 @@ +DockerRequirement | cwl-ts-auto
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Class DockerRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#DockerRequirement

+

Indicates that a workflow component should be run in a +Docker or Docker-compatible (such as +Singularity and udocker) container environment and +specifies how to fetch or build the image.

+

If a CommandLineTool lists DockerRequirement under +hints (or requirements), it may (or must) be run in the specified Docker +container.

+

The platform must first acquire or install the correct Docker image as +specified by dockerPull, dockerImport, dockerLoad or dockerFile.

+

The platform must execute the tool in the container using docker run with +the appropriate Docker image and tool command line.

+

The workflow platform may provide input files and the designated output +directory through the use of volume bind mounts. The platform should rewrite +file paths in the input object to correspond to the Docker bind mounted +locations. That is, the platform should rewrite values in the parameter context +such as runtime.outdir, runtime.tmpdir and others to be valid paths +within the container. The platform must ensure that runtime.outdir and +runtime.tmpdir are distinct directories.

+

When running a tool contained in Docker, the workflow platform must not +assume anything about the contents of the Docker container, such as the +presence or absence of specific software, except to assume that the +generated command line represents a valid command within the runtime +environment of the container.

+

A container image may specify an +ENTRYPOINT +and/or +CMD. +Command line arguments will be appended after all elements of +ENTRYPOINT, and will override all elements specified using CMD (in +other words, CMD is only used when the CommandLineTool definition +produces an empty command line).

+

Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility +concerns of the implicit hidden execution point (For further discussion, see +https://doi.org/10.12688/f1000research.15140.1). Portable +CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. +CommandLineTools which do rely on ENTRYPOINT or CMD must list DockerRequirement in the +requirements section.

+ + +

Interaction with other requirements

+ +

If EnvVarRequirement is specified alongside a +DockerRequirement, the environment variables must be provided to Docker +using --env or --env-file and interact with the container's preexisting +environment as defined by Docker.

+

Hierarchy

  • Saveable
    • DockerRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: DOCKERREQUIREMENT
+

Always 'DockerRequirement'

+

Optional dockerFile

dockerFile?: string
+

Supply the contents of a Dockerfile which will be built using docker build.

+

Optional dockerImageId

dockerImageId?: string
+

The image id that will be used for docker run. May be a +human-readable image name or the image identifier hash. May be skipped +if dockerPull is specified, in which case the dockerPull image id +must be used.

+

Optional dockerImport

dockerImport?: string
+

Provide HTTP URL to download and gunzip a Docker images using `docker import.

+

Optional dockerLoad

dockerLoad?: string
+

Specify a HTTP URL from which to download a Docker image using docker load.

+

Optional dockerOutputDirectory

dockerOutputDirectory?: string
+

Set the designated output directory to a specific location inside the +Docker container.

+

Optional dockerPull

dockerPull?: string
+

Specify a Docker image to retrieve using docker pull. Can contain the +immutable digest to ensure an exact container is used: +dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/EnumSchema.html b/docs/classes/EnumSchema.html new file mode 100644 index 0000000..702a105 --- /dev/null +++ b/docs/classes/EnumSchema.html @@ -0,0 +1,21 @@ +EnumSchema | cwl-ts-auto
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Class EnumSchema

+

Auto-generated class implementation for https://w3id.org/cwl/salad#EnumSchema

+

Define an enumerated type.

+

Hierarchy

  • Saveable
    • EnumSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/EnvVarRequirement.html b/docs/classes/EnvVarRequirement.html new file mode 100644 index 0000000..43a3952 --- /dev/null +++ b/docs/classes/EnvVarRequirement.html @@ -0,0 +1,22 @@ +EnvVarRequirement | cwl-ts-auto
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Class EnvVarRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#EnvVarRequirement

+

Define a list of environment variables which will be set in the +execution environment of the tool. See EnvironmentDef for details.

+

Hierarchy

  • Saveable
    • EnvVarRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: ENVVARREQUIREMENT
+

Always 'EnvVarRequirement'

+

envDef

envDef: EnvironmentDef[]
+

The list of environment variables.

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/EnvironmentDef.html b/docs/classes/EnvironmentDef.html new file mode 100644 index 0000000..54070d7 --- /dev/null +++ b/docs/classes/EnvironmentDef.html @@ -0,0 +1,23 @@ +EnvironmentDef | cwl-ts-auto
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Class EnvironmentDef

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#EnvironmentDef

+

Define an environment variable that will be set in the runtime environment +by the workflow platform when executing the command line tool. May be the +result of executing an expression, such as getting a parameter from input.

+

Hierarchy

  • Saveable
    • EnvironmentDef

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

envName

envName: string
+

The environment variable name

+

envValue

envValue: string
+

The environment variable value

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ExpressionTool.html b/docs/classes/ExpressionTool.html new file mode 100644 index 0000000..21b4230 --- /dev/null +++ b/docs/classes/ExpressionTool.html @@ -0,0 +1,74 @@ +ExpressionTool | cwl-ts-auto
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Class ExpressionTool

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionTool

+

An ExpressionTool is a type of Process object that can be run by itself +or as a Workflow step. It executes a pure Javascript expression that has +access to the same input parameters as a workflow. It is meant to be used +sparingly as a way to isolate complex Javascript expressions that need to +operate on input data and produce some result; perhaps just a +rearrangement of the inputs. No Docker software container is required +or allowed.

+

Hierarchy

  • Saveable
    • ExpressionTool

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: EXPRESSIONTOOL

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

expression

expression: string
+

The expression to execute. The expression must return a plain +Javascript object which matches the output parameters of the +ExpressionTool.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: WorkflowInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: ExpressionToolOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ExpressionToolOutputParameter.html b/docs/classes/ExpressionToolOutputParameter.html new file mode 100644 index 0000000..ec753f9 --- /dev/null +++ b/docs/classes/ExpressionToolOutputParameter.html @@ -0,0 +1,73 @@ +ExpressionToolOutputParameter | cwl-ts-auto
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Class ExpressionToolOutputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter

+

Hierarchy

  • Saveable
    • ExpressionToolOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/File.html b/docs/classes/File.html new file mode 100644 index 0000000..538656c --- /dev/null +++ b/docs/classes/File.html @@ -0,0 +1,180 @@ +File | cwl-ts-auto
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Class File

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#File

+

Represents a file (or group of files when secondaryFiles is provided) that +will be accessible by tools using standard POSIX file system call API such as +open(2) and read(2).

+

Files are represented as objects with class of File. File objects have +a number of properties that provide metadata about the file.

+

The location property of a File is a URI that uniquely identifies the +file. Implementations must support the file:// URI scheme and may support +other schemes such as http://. The value of location may also be a +relative reference, in which case it must be resolved relative to the URI +of the document it appears in. Alternately to location, implementations +must also accept the path property on File, which must be a filesystem +path available on the same host as the CWL runner (for inputs) or the +runtime environment of a command line tool execution (for command line tool +outputs).

+

If no location or path is specified, a file object must specify +contents with the UTF-8 text content of the file. This is a "file +literal". File literals do not correspond to external resources, but are +created on disk with contents with when needed for a executing a tool. +Where appropriate, expressions can return file literals to define new files +on a runtime. The maximum size of contents is 64 kilobytes.

+

The basename property defines the filename on disk where the file is +staged. This may differ from the resource name. If not provided, +basename must be computed from the last path part of location and made +available to expressions.

+

The secondaryFiles property is a list of File or Directory objects that +must be staged in the same directory as the primary file. It is an error +for file names to be duplicated in secondaryFiles.

+

The size property is the size in bytes of the File. It must be computed +from the resource and made available to expressions. The checksum field +contains a cryptographic hash of the file content for use it verifying file +contents. Implementations may, at user option, enable or disable +computation of the checksum field for performance or other reasons. +However, the ability to compute output checksums is required to pass the +CWL conformance test suite.

+

When executing a CommandLineTool, the files and secondary files may be +staged to an arbitrary directory, but must use the value of basename for +the filename. The path property must be file path in the context of the +tool execution runtime (local to the compute node, or within the executing +container). All computed properties should be available to expressions. +File literals also must be staged and path must be set.

+

When collecting CommandLineTool outputs, glob matching returns file paths +(with the path property) and the derived properties. This can all be +modified by outputEval. Alternately, if the file cwl.output.json is +present in the output, outputBinding is ignored.

+

File objects in the output must provide either a location URI or a path +property in the context of the tool execution runtime (local to the compute +node, or within the executing container).

+

When evaluating an ExpressionTool, file objects must be referenced via +location (the expression tool does not have access to files on disk so +path is meaningless) or as file literals. It is legal to return a file +object with an existing location but a different basename. The +loadContents field of ExpressionTool inputs behaves the same as on +CommandLineTool inputs, however it is not meaningful on the outputs.

+

An ExpressionTool may forward file references from input to output by using +the same value for location.

+

Hierarchy

  • Saveable
    • File

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional basename

basename?: string
+

The base name of the file, that is, the name of the file without any +leading directory path. The base name must not contain a slash /.

+

If not provided, the implementation must set this field based on the +location field by taking the final path component after parsing +location as an IRI. If basename is provided, it is not required to +match the value from location.

+

When this file is made available to a CommandLineTool, it must be named +with basename, i.e. the final component of the path field must match +basename.

+

Optional checksum

checksum?: string
+

Optional hash code for validating file integrity. Currently must be in the form +"sha1$ + hexadecimal string" using the SHA-1 algorithm.

+

class_

class_: FILE
+

Must be File to indicate this object describes a file.

+

Optional contents

contents?: string
+

File contents literal.

+

If neither location nor path is provided, contents must be +non-null. The implementation must assign a unique identifier for the +location field. When the file is staged as input to CommandLineTool, +the value of contents must be written to a file.

+

If contents is set as a result of an Javascript expression, +an entry in InitialWorkDirRequirement, or read in from +cwl.output.json, there is no specified upper limit on the +size of contents. Implementations may have practical limits +on the size of contents based on memory and storage +available to the workflow runner or other factors.

+

If the loadContents field of an InputParameter or +OutputParameter is true, and the input or output File object +location is valid, the file must be a UTF-8 text file 64 KiB +or smaller, and the implementation must read the entire +contents of the file and place it in the contents field. If +the size of the file is greater than 64 KiB, the +implementation must raise a fatal error.

+

Optional dirname

dirname?: string
+

The name of the directory containing file, that is, the path leading up +to the final slash in the path such that dirname + '/' + basename == path.

+

The implementation must set this field based on the value of path +prior to evaluating parameter references or expressions in a +CommandLineTool document. This field must not be used in any other +context.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

The format of the file: this must be an IRI of a concept node that +represents the file format, preferrably defined within an ontology. +If no ontology is available, file formats may be tested by exact match.

+

Reasoning about format compatability must be done by checking that an +input file format is the same, owl:equivalentClass or +rdfs:subClassOf the format required by the input parameter. +owl:equivalentClass is transitive with rdfs:subClassOf, e.g. if +<B> owl:equivalentClass <C> and <B> owl:subclassOf <A> then infer +<C> owl:subclassOf <A>.

+

File format ontologies may be provided in the "$schemas" metadata at the +root of the document. If no ontologies are specified in $schemas, the +runtime may perform exact file format matches.

+

loadingOptions

loadingOptions: LoadingOptions

Optional location

location?: string
+

An IRI that identifies the file resource. This may be a relative +reference, in which case it must be resolved using the base IRI of the +document. The location may refer to a local or remote resource; the +implementation must use the IRI to retrieve file content. If an +implementation is unable to retrieve the file content stored at a +remote resource (due to unsupported protocol, access denied, or other +issue) it must signal an error.

+

If the location field is not provided, the contents field must be +provided. The implementation must assign a unique identifier for +the location field.

+

If the path field is provided but the location field is not, an +implementation may assign the value of the path field to location, +then follow the rules above.

+

Optional nameext

nameext?: string
+

The basename extension such that nameroot + nameext == basename, and +nameext is empty or begins with a period and contains at most one +period. Leading periods on the basename are ignored; a basename of +.cshrc will have an empty nameext.

+

The implementation must set this field automatically based on the value +of basename prior to evaluating parameter references or expressions.

+

Optional nameroot

nameroot?: string
+

The basename root such that nameroot + nameext == basename, and +nameext is empty or begins with a period and contains at most one +period. For the purposess of path splitting leading periods on the +basename are ignored; a basename of .cshrc will have a nameroot of +.cshrc.

+

The implementation must set this field automatically based on the value +of basename prior to evaluating parameter references or expressions.

+

Optional path

path?: string
+

The local host path where the File is available when a CommandLineTool is +executed. This field must be set by the implementation. The final +path component must match the value of basename. This field +must not be used in any other context. The command line tool being +executed must be able to to access the file at path using the POSIX +open(2) syscall.

+

As a special case, if the path field is provided but the location +field is not, an implementation may assign the value of the path +field to location, and remove the path field.

+

If the path contains POSIX shell metacharacters +(|,&, ;, <, >, (,), $,`, \, ", ', +<space>, <tab>, and <newline>) or characters +not allowed +for Internationalized Domain Names for Applications +then implementations may terminate the process with a +permanentFailure.

+

Optional secondaryFiles

secondaryFiles?: (File | Directory)[]
+

A list of additional files or directories that are associated with the +primary file and must be transferred alongside the primary file. +Examples include indexes of the primary file, or external references +which must be included when loading primary document. A file object +listed in secondaryFiles may itself include secondaryFiles for +which the same rules apply.

+

Optional size

size?: number
+

Optional file size (in bytes)

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InitialWorkDirRequirement.html b/docs/classes/InitialWorkDirRequirement.html new file mode 100644 index 0000000..2b62eb8 --- /dev/null +++ b/docs/classes/InitialWorkDirRequirement.html @@ -0,0 +1,38 @@ +InitialWorkDirRequirement | cwl-ts-auto
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Class InitialWorkDirRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InitialWorkDirRequirement

+

Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool. +Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for Dirent.entryname. Together with DockerRequirement.dockerOutputDirectory this it possible to control the locations of both input and output files when running in containers.

+

Hierarchy

  • Saveable
    • InitialWorkDirRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: INITIALWORKDIRREQUIREMENT
+

InitialWorkDirRequirement

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional listing

listing?: string | (undefined | string | File | Directory | (File | Directory)[] | Dirent)[]
+

The list of files or subdirectories that must be staged prior +to executing the command line tool.

+

Return type of each expression must validate as ["null", File, Directory, Dirent, {type: array, items: [File, Directory]}].

+

Each File or Directory that is returned by an Expression +must be added to the designated output directory prior to +executing the tool.

+

Each Dirent record that is listed or returned by an +expression specifies a file to be created or staged in the +designated output directory prior to executing the tool.

+

Expressions may return null, in which case they have no effect.

+

Files or Directories which are listed in the input parameters +and appear in the InitialWorkDirRequirement listing must +have their path set to their staged location. If the same +File or Directory appears more than once in the +InitialWorkDirRequirement listing, the implementation must +choose exactly one value for path; how this value is chosen +is undefined.

+

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InlineJavascriptRequirement.html b/docs/classes/InlineJavascriptRequirement.html new file mode 100644 index 0000000..236bc79 --- /dev/null +++ b/docs/classes/InlineJavascriptRequirement.html @@ -0,0 +1,25 @@ +InlineJavascriptRequirement | cwl-ts-auto
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Class InlineJavascriptRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InlineJavascriptRequirement

+

Indicates that the workflow platform must support inline Javascript expressions. +If this requirement is not present, the workflow platform must not perform expression +interpolatation.

+

Hierarchy

  • Saveable
    • InlineJavascriptRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: INLINEJAVASCRIPTREQUIREMENT
+

Always 'InlineJavascriptRequirement'

+

Optional expressionLib

expressionLib?: string[]
+

Additional code fragments that will also be inserted +before executing the expression code. Allows for function definitions that may +be called from CWL expressions.

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InplaceUpdateRequirement.html b/docs/classes/InplaceUpdateRequirement.html new file mode 100644 index 0000000..101af5b --- /dev/null +++ b/docs/classes/InplaceUpdateRequirement.html @@ -0,0 +1,42 @@ +InplaceUpdateRequirement | cwl-ts-auto
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Class InplaceUpdateRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InplaceUpdateRequirement

+

If inplaceUpdate is true, then an implementation supporting this +feature may permit tools to directly update files with writable: true in InitialWorkDirRequirement. That is, as an optimization, +files may be destructively modified in place as opposed to copied +and updated.

+

An implementation must ensure that only one workflow step may +access a writable file at a time. It is an error if a file which +is writable by one workflow step file is accessed (for reading or +writing) by any other workflow step running independently. +However, a file which has been updated in a previous completed +step may be used as input to multiple steps, provided it is +read-only in every step.

+

Workflow steps which modify a file must produce the modified file +as output. Downstream steps which futher process the file must +use the output of previous steps, and not refer to a common input +(this is necessary for both ordering and correctness).

+

Workflow authors should provide this in the hints section. The +intent of this feature is that workflows produce the same results +whether or not InplaceUpdateRequirement is supported by the +implementation, and this feature is primarily available as an +optimization for particular environments.

+

Users and implementers should be aware that workflows that +destructively modify inputs may not be repeatable or reproducible. +In particular, enabling this feature implies that WorkReuse should +not be enabled.

+

Hierarchy

  • Saveable
    • InplaceUpdateRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: INPLACEUPDATEREQUIREMENT
+

Always 'InplaceUpdateRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

inplaceUpdate

inplaceUpdate: boolean

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InputArraySchema.html b/docs/classes/InputArraySchema.html new file mode 100644 index 0000000..cc312f3 --- /dev/null +++ b/docs/classes/InputArraySchema.html @@ -0,0 +1,26 @@ +InputArraySchema | cwl-ts-auto
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Class InputArraySchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema

+

Hierarchy

  • Saveable
    • InputArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InputBinding.html b/docs/classes/InputBinding.html new file mode 100644 index 0000000..d72c59f --- /dev/null +++ b/docs/classes/InputBinding.html @@ -0,0 +1,20 @@ +InputBinding | cwl-ts-auto
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Class InputBinding

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding

+

Hierarchy

  • Saveable
    • InputBinding

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional loadContents

loadContents?: boolean
+

Use of loadContents in InputBinding is deprecated. +Preserved for v1.0 backwards compatability. Will be removed in +CWL v2.0. Use InputParameter.loadContents instead.

+

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InputEnumSchema.html b/docs/classes/InputEnumSchema.html new file mode 100644 index 0000000..4d84604 --- /dev/null +++ b/docs/classes/InputEnumSchema.html @@ -0,0 +1,26 @@ +InputEnumSchema | cwl-ts-auto
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Class InputEnumSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema

+

Hierarchy

  • Saveable
    • InputEnumSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InputRecordField.html b/docs/classes/InputRecordField.html new file mode 100644 index 0000000..37fefb9 --- /dev/null +++ b/docs/classes/InputRecordField.html @@ -0,0 +1,93 @@ +InputRecordField | cwl-ts-auto
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Class InputRecordField

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField

+

Hierarchy

  • Saveable
    • InputRecordField

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

name

name: string
+

The name of the field

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

The field type

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/InputRecordSchema.html b/docs/classes/InputRecordSchema.html new file mode 100644 index 0000000..612cedb --- /dev/null +++ b/docs/classes/InputRecordSchema.html @@ -0,0 +1,26 @@ +InputRecordSchema | cwl-ts-auto
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Class InputRecordSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema

+

Hierarchy

  • Saveable
    • InputRecordSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: InputRecordField[]
+

Defines the fields of the record.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/LoadListingRequirement.html b/docs/classes/LoadListingRequirement.html new file mode 100644 index 0000000..b6392ab --- /dev/null +++ b/docs/classes/LoadListingRequirement.html @@ -0,0 +1,20 @@ +LoadListingRequirement | cwl-ts-auto
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Class LoadListingRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#LoadListingRequirement

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

Hierarchy

  • Saveable
    • LoadListingRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: LOADLISTINGREQUIREMENT
+

Always 'LoadListingRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional loadListing

loadListing?: LoadListingEnum

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/MultipleInputFeatureRequirement.html b/docs/classes/MultipleInputFeatureRequirement.html new file mode 100644 index 0000000..8e6c41d --- /dev/null +++ b/docs/classes/MultipleInputFeatureRequirement.html @@ -0,0 +1,20 @@ +MultipleInputFeatureRequirement | cwl-ts-auto
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Class MultipleInputFeatureRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement

+

Indicates that the workflow platform must support multiple inbound data links +listed in the source field of WorkflowStepInput.

+

Hierarchy

  • Saveable
    • MultipleInputFeatureRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: MULTIPLEINPUTFEATUREREQUIREMENT
+

Always 'MultipleInputFeatureRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/NetworkAccess.html b/docs/classes/NetworkAccess.html new file mode 100644 index 0000000..c29811f --- /dev/null +++ b/docs/classes/NetworkAccess.html @@ -0,0 +1,30 @@ +NetworkAccess | cwl-ts-auto
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Class NetworkAccess

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#NetworkAccess

+

Indicate whether a process requires outgoing IPv4/IPv6 network +access. Choice of IPv4 or IPv6 is implementation and site +specific, correct tools must support both.

+

If networkAccess is false or not specified, tools must not +assume network access, except for localhost (the loopback device).

+

If networkAccess is true, the tool must be able to make outgoing +connections to network resources. Resources may be on a private +subnet or the public Internet. However, implementations and sites +may apply their own security policies to restrict what is +accessible by the tool.

+

Enabling network access does not imply a publically routable IP +address or the ability to accept inbound connections.

+

Hierarchy

  • Saveable
    • NetworkAccess

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: NETWORKACCESS
+

Always 'NetworkAccess'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

networkAccess

networkAccess: string | boolean

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/Operation.html b/docs/classes/Operation.html new file mode 100644 index 0000000..a469642 --- /dev/null +++ b/docs/classes/Operation.html @@ -0,0 +1,70 @@ +Operation | cwl-ts-auto
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Class Operation

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#Operation

+

This record describes an abstract operation. It is a potential +step of a workflow that has not yet been bound to a concrete +implementation. It specifies an input and output signature, but +does not provide enough information to be executed. An +implementation (or other tooling) may provide a means of binding +an Operation to a concrete process (such as Workflow, +CommandLineTool, or ExpressionTool) with a compatible signature.

+

Hierarchy

  • Saveable
    • Operation

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: OPERATION

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: OperationInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: OperationOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/OperationInputParameter.html b/docs/classes/OperationInputParameter.html new file mode 100644 index 0000000..3ecd67c --- /dev/null +++ b/docs/classes/OperationInputParameter.html @@ -0,0 +1,99 @@ +OperationInputParameter | cwl-ts-auto
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Class OperationInputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#OperationInputParameter

+

Describe an input parameter of an operation.

+

Hierarchy

  • Saveable
    • OperationInputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/OperationOutputParameter.html b/docs/classes/OperationOutputParameter.html new file mode 100644 index 0000000..8d1549a --- /dev/null +++ b/docs/classes/OperationOutputParameter.html @@ -0,0 +1,74 @@ +OperationOutputParameter | cwl-ts-auto
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Class OperationOutputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#OperationOutputParameter

+

Describe an output parameter of an operation.

+

Hierarchy

  • Saveable
    • OperationOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/OutputArraySchema.html b/docs/classes/OutputArraySchema.html new file mode 100644 index 0000000..d6aeba8 --- /dev/null +++ b/docs/classes/OutputArraySchema.html @@ -0,0 +1,26 @@ +OutputArraySchema | cwl-ts-auto
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Class OutputArraySchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema

+

Hierarchy

  • Saveable
    • OutputArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/OutputEnumSchema.html b/docs/classes/OutputEnumSchema.html new file mode 100644 index 0000000..3e26f18 --- /dev/null +++ b/docs/classes/OutputEnumSchema.html @@ -0,0 +1,26 @@ +OutputEnumSchema | cwl-ts-auto
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Class OutputEnumSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema

+

Hierarchy

  • Saveable
    • OutputEnumSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/OutputRecordField.html b/docs/classes/OutputRecordField.html new file mode 100644 index 0000000..3071f60 --- /dev/null +++ b/docs/classes/OutputRecordField.html @@ -0,0 +1,73 @@ +OutputRecordField | cwl-ts-auto
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Class OutputRecordField

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField

+

Hierarchy

  • Saveable
    • OutputRecordField

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

name

name: string
+

The name of the field

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

The field type

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/OutputRecordSchema.html b/docs/classes/OutputRecordSchema.html new file mode 100644 index 0000000..c95ffa9 --- /dev/null +++ b/docs/classes/OutputRecordSchema.html @@ -0,0 +1,26 @@ +OutputRecordSchema | cwl-ts-auto
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Class OutputRecordSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema

+

Hierarchy

  • Saveable
    • OutputRecordSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: OutputRecordField[]
+

Defines the fields of the record.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/RecordField.html b/docs/classes/RecordField.html new file mode 100644 index 0000000..fa14b4a --- /dev/null +++ b/docs/classes/RecordField.html @@ -0,0 +1,23 @@ +RecordField | cwl-ts-auto
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Class RecordField

+

Auto-generated class implementation for https://w3id.org/cwl/salad#RecordField

+

A field of a record.

+

Hierarchy

  • Saveable
    • RecordField

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

name

name: string
+

The name of the field

+

type

type: string | RecordSchema | EnumSchema | ArraySchema | (string | RecordSchema | EnumSchema | ArraySchema)[]
+

The field type

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/RecordSchema.html b/docs/classes/RecordSchema.html new file mode 100644 index 0000000..2904716 --- /dev/null +++ b/docs/classes/RecordSchema.html @@ -0,0 +1,20 @@ +RecordSchema | cwl-ts-auto
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Class RecordSchema

+

Auto-generated class implementation for https://w3id.org/cwl/salad#RecordSchema

+

Hierarchy

  • Saveable
    • RecordSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: RecordField[]
+

Defines the fields of the record.

+

loadingOptions

loadingOptions: LoadingOptions

type

type: RECORD
+

Must be record

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ResourceRequirement.html b/docs/classes/ResourceRequirement.html new file mode 100644 index 0000000..dc4ce09 --- /dev/null +++ b/docs/classes/ResourceRequirement.html @@ -0,0 +1,90 @@ +ResourceRequirement | cwl-ts-auto
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Class ResourceRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#ResourceRequirement

+

Specify basic hardware resource requirements.

+

"min" is the minimum amount of a resource that must be reserved to +schedule a job. If "min" cannot be satisfied, the job should not +be run.

+

"max" is the maximum amount of a resource that the job shall be +allocated. If a node has sufficient resources, multiple jobs may +be scheduled on a single node provided each job's "max" resource +requirements are met. If a job attempts to exceed its resource +allocation, an implementation may deny additional resources, which +may result in job failure.

+

If both "min" and "max" are specified, an implementation may +choose to allocate any amount between "min" and "max", with the +actual allocation provided in the runtime object.

+

If "min" is specified but "max" is not, then "max" == "min" +If "max" is specified by "min" is not, then "min" == "max".

+

It is an error if max < min.

+

It is an error if the value of any of these fields is negative.

+

If neither "min" nor "max" is specified for a resource, use the default values below.

+

Hierarchy

  • Saveable
    • ResourceRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: RESOURCEREQUIREMENT
+

Always 'ResourceRequirement'

+

Optional coresMax

coresMax?: string | number
+

Maximum reserved number of CPU cores.

+

See coresMin for discussion about fractional CPU requests.

+

Optional coresMin

coresMin?: string | number
+

Minimum reserved number of CPU cores (default is 1).

+

May be a fractional value to indicate to a scheduling +algorithm that one core can be allocated to multiple +jobs. For example, a value of 0.25 indicates that up to 4 +jobs may run in parallel on 1 core. A value of 1.25 means +that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3).

+

Processes can only share a core allocation if the sum of each +of their ramMax, tmpdirMax, and outdirMax requests also +do not exceed the capacity of the node.

+

Processes sharing a core must have the same level of isolation +(typically a container or VM) that they would normally.

+

The reported number of CPU cores reserved for the process, +which is available to expressions on the CommandLineTool as +runtime.cores, must be a non-zero integer, and may be +calculated by rounding up the cores request to the next whole +number.

+

Scheduling systems may allocate fractional CPU resources by +setting quotas or scheduling weights. Scheduling systems that +do not support fractional CPUs may round up the request to the +next whole number.

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Optional outdirMax

outdirMax?: string | number
+

Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

+

See outdirMin for discussion about fractional storage requests.

+

Optional outdirMin

outdirMin?: string | number
+

Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)

+

May be a fractional value. If so, the actual storage request +must be rounded up to the next whole number. The reported +amount of storage reserved for the process, which is available +to expressions on the CommandLineTool as runtime.outdirSize, +must be a non-zero integer.

+

Optional ramMax

ramMax?: string | number
+

Maximum reserved RAM in mebibytes (2**20)

+

See ramMin for discussion about fractional RAM requests.

+

Optional ramMin

ramMin?: string | number
+

Minimum reserved RAM in mebibytes (2**20) (default is 256)

+

May be a fractional value. If so, the actual RAM request must +be rounded up to the next whole number. The reported amount of +RAM reserved for the process, which is available to +expressions on the CommandLineTool as runtime.ram, must be a +non-zero integer.

+

Optional tmpdirMax

tmpdirMax?: string | number
+

Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

+

See tmpdirMin for discussion about fractional storage requests.

+

Optional tmpdirMin

tmpdirMin?: string | number
+

Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)

+

May be a fractional value. If so, the actual storage request +must be rounded up to the next whole number. The reported +amount of storage reserved for the process, which is available +to expressions on the CommandLineTool as runtime.tmpdirSize, +must be a non-zero integer.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ScatterFeatureRequirement.html b/docs/classes/ScatterFeatureRequirement.html new file mode 100644 index 0000000..701212b --- /dev/null +++ b/docs/classes/ScatterFeatureRequirement.html @@ -0,0 +1,20 @@ +ScatterFeatureRequirement | cwl-ts-auto
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Class ScatterFeatureRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#ScatterFeatureRequirement

+

Indicates that the workflow platform must support the scatter and +scatterMethod fields of WorkflowStep.

+

Hierarchy

  • Saveable
    • ScatterFeatureRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: SCATTERFEATUREREQUIREMENT
+

Always 'ScatterFeatureRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/SchemaDefRequirement.html b/docs/classes/SchemaDefRequirement.html new file mode 100644 index 0000000..0f9dc20 --- /dev/null +++ b/docs/classes/SchemaDefRequirement.html @@ -0,0 +1,33 @@ +SchemaDefRequirement | cwl-ts-auto
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Class SchemaDefRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#SchemaDefRequirement

+

This field consists of an array of type definitions which must be used when +interpreting the inputs and outputs fields. When a type field +contains a IRI, the implementation must check if the type is defined in +schemaDefs and use that definition. If the type is not found in +schemaDefs, it is an error. The entries in schemaDefs must be +processed in the order listed such that later schema definitions may refer +to earlier schema definitions.

+
    +
  • Type definitions are allowed for enum and record types only.
    • +
  • Type definitions may be shared by defining them in a file and then +$include-ing them in the types field.
    • +
  • A file can contain a list of type definitions
    • +
+

Hierarchy

  • Saveable
    • SchemaDefRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: SCHEMADEFREQUIREMENT
+

Always 'SchemaDefRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

types

types: (CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

The list of type definitions.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/SecondaryFileSchema.html b/docs/classes/SecondaryFileSchema.html new file mode 100644 index 0000000..92a9e0a --- /dev/null +++ b/docs/classes/SecondaryFileSchema.html @@ -0,0 +1,79 @@ +SecondaryFileSchema | cwl-ts-auto
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Class SecondaryFileSchema

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#SecondaryFileSchema

+

Secondary files are specified using the following micro-DSL for secondary files:

+
    +
  • If the value is a string, it is transformed to an object with two fields +pattern and required
    • +
  • By default, the value of required is null +(this indicates default behavior, which may be based on the context)
    • +
  • If the value ends with a question mark ? the question mark is +stripped off and the value of the field required is set to False
    • +
  • The remaining value is assigned to the field pattern
    • +
+

For implementation details and examples, please see +this section +in the Schema Salad specification.

+

Hierarchy

  • Saveable
    • SecondaryFileSchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

pattern

pattern: string
+

Provides a pattern or expression specifying files or directories that +should be included alongside the primary file.

+

If the value is an expression, the value of self in the +expression must be the primary input or output File object to +which this binding applies. The basename, nameroot and +nameext fields must be present in self. For +CommandLineTool inputs the location field must also be +present. For CommandLineTool outputs the path field must +also be present. If secondary files were included on an input +File object as part of the Process invocation, they must also +be present in secondaryFiles on self.

+

The expression must return either: a filename string relative +to the path to the primary File, a File or Directory object +(class: File or class: Directory) with either location +(for inputs) or path (for outputs) and basename fields +set, or an array consisting of strings or File or Directory +objects as previously described.

+

It is legal to use location from a File or Directory object +passed in as input, including location from secondary files +on self. If an expression returns a File object with the +same location but a different basename as a secondary file +that was passed in, the expression result takes precedence. +Setting the basename with an expression this way affects the +path where the secondary file will be staged to in the +CommandLineTool.

+

The expression may return "null" in which case there is no +secondary file from that expression.

+

To work on non-filename-preserving storage systems, portable +tool descriptions should treat location as an opaque +identifier and avoid constructing new values from location, +but should construct relative references using basename or +nameroot instead, or propagate location from defined inputs.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional required

required?: string | boolean
+

An implementation must not fail workflow execution if required is +set to false and the expected secondary file does not exist. +Default value for required field is true for secondary files on +input and false for secondary files on output.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ShellCommandRequirement.html b/docs/classes/ShellCommandRequirement.html new file mode 100644 index 0000000..3c0fe21 --- /dev/null +++ b/docs/classes/ShellCommandRequirement.html @@ -0,0 +1,25 @@ +ShellCommandRequirement | cwl-ts-auto
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Class ShellCommandRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#ShellCommandRequirement

+

Modify the behavior of CommandLineTool to generate a single string +containing a shell command line. Each item in the argument list must be +joined into a string separated by single spaces and quoted to prevent +intepretation by the shell, unless CommandLineBinding for that argument +contains shellQuote: false. If shellQuote: false is specified, the +argument is joined into the command string without quoting, which allows +the use of shell metacharacters such as | for pipes.

+

Hierarchy

  • Saveable
    • ShellCommandRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: SHELLCOMMANDREQUIREMENT
+

Always 'ShellCommandRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/SoftwarePackage.html b/docs/classes/SoftwarePackage.html new file mode 100644 index 0000000..b27a76a --- /dev/null +++ b/docs/classes/SoftwarePackage.html @@ -0,0 +1,60 @@ +SoftwarePackage | cwl-ts-auto
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Class SoftwarePackage

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage

+

Hierarchy

  • Saveable
    • SoftwarePackage

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

package_

package_: string
+

The name of the software to be made available. If the name is +common, inconsistent, or otherwise ambiguous it should be combined with +one or more identifiers in the specs field.

+

Optional specs

specs?: string[]
+

One or more IRIs +identifying resources for installing or enabling the software named in +the package field. Implementations may provide resolvers which map +these software identifer IRIs to some configuration action; or they can +use only the name from the package field on a best effort basis.

+

For example, the IRI https://packages.debian.org/bowtie could +be resolved with apt-get install bowtie. The IRI +https://anaconda.org/bioconda/bowtie could be resolved with conda install -c bioconda bowtie.

+

IRIs can also be system independent and used to map to a specific +software installation or selection mechanism. +Using RRID as an example: +https://identifiers.org/rrid/RRID:SCR_005476 +could be fulfilled using the above mentioned Debian or bioconda +package, a local installation managed by Environment Modules, +or any other mechanism the platform chooses. IRIs can also be from +identifer sources that are discipline specific yet still system +independent. As an example, the equivalent ELIXIR Tools and Data +Service Registry IRI to the previous RRID example is +https://bio.tools/tool/bowtie2/version/2.2.8. +If supported by a given registry, implementations are encouraged to +query these system independent sofware identifier IRIs directly for +links to packaging systems.

+

A site specific IRI can be listed as well. For example, an academic +computing cluster using Environment Modules could list the IRI +https://hpc.example.edu/modules/bowtie-tbb/1.22 to indicate that +module load bowtie-tbb/1.1.2 should be executed to make available +bowtie version 1.1.2 compiled with the TBB library prior to running +the accompanying Workflow or CommandLineTool. Note that the example IRI +is specific to a particular institution and computing environment as +the Environment Modules system does not have a common namespace or +standardized naming convention.

+

This last example is the least portable and should only be used if +mechanisms based off of the package field or more generic IRIs are +unavailable or unsuitable. While harmless to other sites, site specific +software IRIs should be left out of shared CWL descriptions to avoid +clutter.

+

Optional version

version?: string[]
+

The (optional) versions of the software that are known to be +compatible.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/SoftwareRequirement.html b/docs/classes/SoftwareRequirement.html new file mode 100644 index 0000000..13a8099 --- /dev/null +++ b/docs/classes/SoftwareRequirement.html @@ -0,0 +1,22 @@ +SoftwareRequirement | cwl-ts-auto
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Class SoftwareRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwareRequirement

+

A list of software packages that should be configured in the environment of +the defined process.

+

Hierarchy

  • Saveable
    • SoftwareRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: SOFTWAREREQUIREMENT
+

Always 'SoftwareRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

packages

packages: SoftwarePackage[]
+

The list of software to be configured.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/StepInputExpressionRequirement.html b/docs/classes/StepInputExpressionRequirement.html new file mode 100644 index 0000000..b77f4cd --- /dev/null +++ b/docs/classes/StepInputExpressionRequirement.html @@ -0,0 +1,20 @@ +StepInputExpressionRequirement | cwl-ts-auto
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Class StepInputExpressionRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#StepInputExpressionRequirement

+

Indicate that the workflow platform must support the valueFrom field +of WorkflowStepInput.

+

Hierarchy

  • Saveable
    • StepInputExpressionRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: STEPINPUTEXPRESSIONREQUIREMENT
+

Always 'StepInputExpressionRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/SubworkflowFeatureRequirement.html b/docs/classes/SubworkflowFeatureRequirement.html new file mode 100644 index 0000000..58b831e --- /dev/null +++ b/docs/classes/SubworkflowFeatureRequirement.html @@ -0,0 +1,20 @@ +SubworkflowFeatureRequirement | cwl-ts-auto
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Class SubworkflowFeatureRequirement

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement

+

Indicates that the workflow platform must support nested workflows in +the run field of WorkflowStep.

+

Hierarchy

  • Saveable
    • SubworkflowFeatureRequirement

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: SUBWORKFLOWFEATUREREQUIREMENT
+

Always 'SubworkflowFeatureRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ToolTimeLimit.html b/docs/classes/ToolTimeLimit.html new file mode 100644 index 0000000..9f52cf1 --- /dev/null +++ b/docs/classes/ToolTimeLimit.html @@ -0,0 +1,28 @@ +ToolTimeLimit | cwl-ts-auto
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Class ToolTimeLimit

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#ToolTimeLimit

+

Set an upper limit on the execution time of a CommandLineTool. +A CommandLineTool whose execution duration exceeds the time +limit may be preemptively terminated and considered failed. +May also be used by batch systems to make scheduling decisions. +The execution duration excludes external operations, such as +staging of files, pulling a docker image etc, and only counts +wall-time for the execution of the command line itself.

+

Hierarchy

  • Saveable
    • ToolTimeLimit

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: TOOLTIMELIMIT
+

Always 'ToolTimeLimit'

+

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

timelimit

timelimit: string | number
+

The time limit, in seconds. A time limit of zero means no +time limit. Negative time limits are an error.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/ValidationException.html b/docs/classes/ValidationException.html new file mode 100644 index 0000000..9337d93 --- /dev/null +++ b/docs/classes/ValidationException.html @@ -0,0 +1,6 @@ +ValidationException | cwl-ts-auto
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Class ValidationException

Hierarchy

  • Error
    • ValidationException

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

bullet

bullet: string = ''

children

children: ValidationException[]

message

message: string

name

name: string

Optional stack

stack?: string

Static indentPerLevel

indentPerLevel: number = 2

Static Optional prepareStackTrace

prepareStackTrace?: (err: Error, stackTraces: CallSite[]) => any

Type declaration

Static stackTraceLimit

stackTraceLimit: number

Methods

prettyStr

  • prettyStr(level?: number): string

simplify

summary

  • summary(level: number): string

toString

  • toString(): string

withBullet

Static captureStackTrace

  • captureStackTrace(targetObject: object, constructorOpt?: Function): void
  • +

    Create .stack property on a target object

    +

    Parameters

    • targetObject: object
    • Optional constructorOpt: Function

    Returns void

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\ No newline at end of file diff --git a/docs/classes/WorkReuse.html b/docs/classes/WorkReuse.html new file mode 100644 index 0000000..55ad29d --- /dev/null +++ b/docs/classes/WorkReuse.html @@ -0,0 +1,26 @@ +WorkReuse | cwl-ts-auto
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Class WorkReuse

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkReuse

+

For implementations that support reusing output from past work (on +the assumption that same code and same input produce same +results), control whether to enable or disable the reuse behavior +for a particular tool or step (to accomodate situations where that +assumption is incorrect). A reused step is not executed but +instead returns the same output as the original execution.

+

If WorkReuse is not specified, correct tools should assume it +is enabled by default.

+

Hierarchy

  • Saveable
    • WorkReuse

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: WORKREUSE
+

Always 'WorkReuse'

+

enableReuse

enableReuse: string | boolean

Optional extensionFields

extensionFields?: Dictionary<any>

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/Workflow.html b/docs/classes/Workflow.html new file mode 100644 index 0000000..222c0af --- /dev/null +++ b/docs/classes/Workflow.html @@ -0,0 +1,119 @@ +Workflow | cwl-ts-auto
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Class Workflow

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#Workflow

+

A workflow describes a set of steps and the dependencies between +those steps. When a step produces output that will be consumed by a +second step, the first step is a dependency of the second step.

+

When there is a dependency, the workflow engine must execute the preceding +step and wait for it to successfully produce output before executing the +dependent step. If two steps are defined in the workflow graph that +are not directly or indirectly dependent, these steps are independent, +and may execute in any order or execute concurrently. A workflow is +complete when all steps have been executed.

+

Dependencies between parameters are expressed using the source +field on workflow step input parameters and +outputSource field on workflow output +parameters.

+

The source field on each workflow step input parameter expresses +the data links that contribute to the value of the step input +parameter (the "sink"). A workflow step can only begin execution +when every data link connected to a step has been fulfilled.

+

The outputSource field on each workflow step input parameter +expresses the data links that contribute to the value of the +workflow output parameter (the "sink"). Workflow execution cannot +complete successfully until every data link connected to an output +parameter has been fulfilled.

+ + +

Workflow success and failure

+ +

A completed step must result in one of success, temporaryFailure or +permanentFailure states. An implementation may choose to retry a step +execution which resulted in temporaryFailure. An implementation may +choose to either continue running other steps of a workflow, or terminate +immediately upon permanentFailure.

+
    +

  • If any step of a workflow execution results in permanentFailure, then +the workflow status is permanentFailure.

    +
    • +

  • If one or more steps result in temporaryFailure and all other steps +complete success or are not executed, then the workflow status is +temporaryFailure.

    +
    • +

  • If all workflow steps are executed and complete with success, then the +workflow status is success.

    +
    • +
+ + +

Extensions

+ +

ScatterFeatureRequirement and +SubworkflowFeatureRequirement are +available as standard extensions to core +workflow semantics.

+

Hierarchy

  • Saveable
    • Workflow

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: WORKFLOW

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: WorkflowInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: WorkflowOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

steps

steps: WorkflowStep[]
+

The individual steps that make up the workflow. Each step is executed when all of its +input data links are fufilled. An implementation may choose to execute +the steps in a different order than listed and/or execute steps +concurrently, provided that dependencies between steps are met.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/WorkflowInputParameter.html b/docs/classes/WorkflowInputParameter.html new file mode 100644 index 0000000..7cc7221 --- /dev/null +++ b/docs/classes/WorkflowInputParameter.html @@ -0,0 +1,101 @@ +WorkflowInputParameter | cwl-ts-auto
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Class WorkflowInputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter

+

Hierarchy

  • Saveable
    • WorkflowInputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional inputBinding

inputBinding?: InputBinding
+

Deprecated. Preserved for v1.0 backwards compatability. Will be removed in +CWL v2.0. Use WorkflowInputParameter.loadContents instead.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/WorkflowOutputParameter.html b/docs/classes/WorkflowOutputParameter.html new file mode 100644 index 0000000..0e76792 --- /dev/null +++ b/docs/classes/WorkflowOutputParameter.html @@ -0,0 +1,87 @@ +WorkflowOutputParameter | cwl-ts-auto
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Class WorkflowOutputParameter

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowOutputParameter

+

Describe an output parameter of a workflow. The parameter must be +connected to one or more parameters defined in the workflow that +will provide the value of the output parameter. It is legal to +connect a WorkflowInputParameter to a WorkflowOutputParameter.

+

See WorkflowStepInput for discussion of +linkMerge and pickValue.

+

Hierarchy

  • Saveable
    • WorkflowOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional linkMerge

linkMerge?: LinkMergeMethod
+

The method to use to merge multiple sources into a single array. +If not specified, the default method is "merge_nested".

+

loadingOptions

loadingOptions: LoadingOptions

Optional outputSource

outputSource?: string | string[]
+

Specifies one or more workflow parameters that supply the value of to +the output parameter.

+

Optional pickValue

pickValue?: PickValueMethod
+

The method to use to choose non-null elements among multiple sources.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/WorkflowStep.html b/docs/classes/WorkflowStep.html new file mode 100644 index 0000000..67d90f9 --- /dev/null +++ b/docs/classes/WorkflowStep.html @@ -0,0 +1,126 @@ +WorkflowStep | cwl-ts-auto
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Class WorkflowStep

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStep

+

A workflow step is an executable element of a workflow. It specifies the +underlying process implementation (such as CommandLineTool or another +Workflow) in the run field and connects the input and output parameters +of the underlying process to workflow parameters.

+ + +

Scatter/gather

+ +

To use scatter/gather, +ScatterFeatureRequirement must be specified +in the workflow or workflow step requirements.

+

A "scatter" operation specifies that the associated workflow step or +subworkflow should execute separately over a list of input elements. Each +job making up a scatter operation is independent and may be executed +concurrently.

+

The scatter field specifies one or more input parameters which will be +scattered. An input parameter may be listed more than once. The declared +type of each input parameter is implicitly becomes an array of items of the +input parameter type. If a parameter is listed more than once, it becomes +a nested array. As a result, upstream parameters which are connected to +scattered parameters must be arrays.

+

All output parameter types are also implicitly wrapped in arrays. Each job +in the scatter results in an entry in the output array.

+

If any scattered parameter runtime value is an empty array, all outputs are +set to empty arrays and no work is done for the step, according to +applicable scattering rules.

+

If scatter declares more than one input parameter, scatterMethod +describes how to decompose the input into a discrete set of jobs.

+
    +

  • dotproduct specifies that each of the input arrays are aligned and one + element taken from each array to construct each job. It is an error + if all input arrays are not the same length.

    +
    • +

  • nested_crossproduct specifies the Cartesian product of the inputs, + producing a job for every combination of the scattered inputs. The + output must be nested arrays for each level of scattering, in the + order that the input arrays are listed in the scatter field.

    +
    • +

  • flat_crossproduct specifies the Cartesian product of the inputs, + producing a job for every combination of the scattered inputs. The + output arrays must be flattened to a single level, but otherwise listed in the + order that the input arrays are listed in the scatter field.

    +
    • +
+ + +

Conditional execution (Optional)

+ +

Conditional execution makes execution of a step conditional on an +expression. A step that is not executed is "skipped". A skipped +step produces null for all output parameters.

+

The condition is evaluated after scatter, using the input object +of each individual scatter job. This means over a set of scatter +jobs, some may be executed and some may be skipped. When the +results are gathered, skipped steps must be null in the output +arrays.

+

The when field controls conditional execution. This is an +expression that must be evaluated with inputs bound to the step +input object (or individual scatter job), and returns a boolean +value. It is an error if this expression returns a value other +than true or false.

+

Conditionals in CWL are an optional feature and are not required +to be implemented by all consumers of CWL documents. An +implementation that does not support conditionals must return a +fatal error when attempting execute a workflow that uses +conditional constructs the implementation does not support.

+ + +

Subworkflows

+ +

To specify a nested workflow as part of a workflow step, +SubworkflowFeatureRequirement must be +specified in the workflow or workflow step requirements.

+

It is a fatal error if a workflow directly or indirectly invokes itself as +a subworkflow (recursive workflows are not allowed).

+

Hierarchy

  • Saveable
    • WorkflowStep

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this workflow step. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

in_

in_: WorkflowStepInput[]
+

Defines the input parameters of the workflow step. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used build a user +interface for constructing the input object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

loadingOptions

loadingOptions: LoadingOptions

out

out: (string | WorkflowStepOutput)[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this workflow step. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

run

run: string | CommandLineTool | ExpressionTool | Workflow | Operation
+

Specifies the process to run.

+

Optional scatter

scatter?: string | string[]

Optional scatterMethod

scatterMethod?: ScatterMethod
+

Required if scatter is an array of more than one element.

+

Optional when

when?: string
+

If defined, only run the step when the expression evaluates to +true. If false the step is skipped. A skipped step +produces a null on each output.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/WorkflowStepInput.html b/docs/classes/WorkflowStepInput.html new file mode 100644 index 0000000..45dc905 --- /dev/null +++ b/docs/classes/WorkflowStepInput.html @@ -0,0 +1,181 @@ +WorkflowStepInput | cwl-ts-auto
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Class WorkflowStepInput

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStepInput

+

The input of a workflow step connects an upstream parameter (from the +workflow inputs, or the outputs of other workflows steps) with the input +parameters of the process specified by the run field. Only input parameters +declared by the target process will be passed through at runtime to the process +though additonal parameters may be specified (for use within valueFrom +expressions for instance) - unconnected or unused parameters do not represent an +error condition.

+ + +

Input object

+ +

A WorkflowStepInput object must contain an id field in the form +#fieldname or #prefix/fieldname. When the id field contains a slash +/ the field name consists of the characters following the final slash +(the prefix portion may contain one or more slashes to indicate scope). +This defines a field of the workflow step input object with the value of +the source parameter(s).

+ + +

Merging multiple inbound data links

+ +

To merge multiple inbound data links, +MultipleInputFeatureRequirement must be specified +in the workflow or workflow step requirements.

+

If the sink parameter is an array, or named in a workflow +scatter operation, there may be multiple inbound +data links listed in the source field. The values from the +input links are merged depending on the method specified in the +linkMerge field. If both linkMerge and pickValue are null +or not specified, and there is more than one element in the +source array, the default method is "merge_nested".

+

If both linkMerge and pickValue are null or not specified, and +there is only a single element in the source, then the input +parameter takes the scalar value from the single input link (it is +not wrapped in a single-list).

+
    +

  • merge_nested

    +

    The input must be an array consisting of exactly one entry for each +input link. If "merge_nested" is specified with a single link, the value +from the link must be wrapped in a single-item list.

    +
    • +

  • merge_flattened

    +
      +
    1. The source and sink parameters must be compatible types, or the source +type must be compatible with single element from the "items" type of +the destination array parameter.
      2. +
    2. Source parameters which are arrays are concatenated. +Source parameters which are single element types are appended as +single elements.
      3. +
    +
    • +
+ + +

Picking non-null values among inbound data links

+ +

If present, pickValue specifies how to picking non-null values among inbound data links.

+

pickValue is evaluated

+
    +
  1. Once all source values from upstream step or parameters are available.
    2. +
  2. After linkMerge.
    3. +
  3. Before scatter or valueFrom.
    4. +
+

This is specifically intended to be useful in combination with +conditional execution, where several upstream +steps may be connected to a single input (source is a list), and +skipped steps produce null values.

+

Static type checkers should check for type consistency after infering what the type +will be after pickValue is applied, just as they do currently for linkMerge.

+
    +

  • first_non_null

    +

    For the first level of a list input, pick the first non-null element. The result is a scalar. +It is an error if there is no non-null element. Examples:

    +
      +
    • [null, x, null, y] -> x
      • +
    • [null, [null], null, y] -> [null]
      • +
    • [null, null, null] -> Runtime Error
      • +
    +

    Intended use case: If-else pattern where the +value comes either from a conditional step or from a default or +fallback value. The conditional step(s) should be placed first in +the list.

    +
    • +

  • the_only_non_null

    +

    For the first level of a list input, pick the single non-null element. The result is a scalar. +It is an error if there is more than one non-null element. Examples:

    +
      +
    • [null, x, null] -> x
      • +
    • [null, x, null, y] -> Runtime Error
      • +
    • [null, [null], null] -> [null]
      • +
    • [null, null, null] -> Runtime Error
      • +
    +

    Intended use case: Switch type patterns where developer considers +more than one active code path as a workflow error +(possibly indicating an error in writing when condition expressions).

    +
    • +

  • all_non_null

    +

    For the first level of a list input, pick all non-null values. +The result is a list, which may be empty. Examples:

    +
      +
    • [null, x, null] -> [x]
      • +
    • [x, null, y] -> [x, y]
      • +
    • [null, [x], [null]] -> [[x], [null]]
      • +
    • [null, null, null] -> []
      • +
    +

    Intended use case: It is valid to have more than one source, but + sources are conditional, so null sources (from skipped steps) + should be filtered out.

    +
    • +
+

Hierarchy

  • Saveable
    • WorkflowStepInput

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional default_

default_?: any
+

The default value for this parameter to use if either there is no +source field, or the value produced by the source is null. The +default must be applied prior to scattering or evaluating valueFrom.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional linkMerge

linkMerge?: LinkMergeMethod
+

The method to use to merge multiple inbound links into a single array. +If not specified, the default method is "merge_nested".

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

loadingOptions

loadingOptions: LoadingOptions

Optional pickValue

pickValue?: PickValueMethod
+

The method to use to choose non-null elements among multiple sources.

+

Optional source

source?: string | string[]
+

Specifies one or more workflow parameters that will provide input to +the underlying step parameter.

+

Optional valueFrom

valueFrom?: string
+

To use valueFrom, StepInputExpressionRequirement must +be specified in the workflow or workflow step requirements.

+

If valueFrom is a constant string value, use this as the value for +this input parameter.

+

If valueFrom is a parameter reference or expression, it must be +evaluated to yield the actual value to be assiged to the input field.

+

The self value in the parameter reference or expression must be

+
    +
  1. null if there is no source field
    2. +
  2. the value of the parameter(s) specified in the source field when this +workflow input parameter is not specified in this workflow step's scatter field.
    3. +
  3. an element of the parameter specified in the source field when this workflow input +parameter is specified in this workflow step's scatter field.
    4. +
+

The value of inputs in the parameter reference or expression must be +the input object to the workflow step after assigning the source +values, applying default, and then scattering. The order of +evaluating valueFrom among step input parameters is undefined and the +result of evaluating valueFrom on a parameter must not be visible to +evaluation of valueFrom on other parameters.

+

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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\ No newline at end of file diff --git a/docs/classes/WorkflowStepOutput.html b/docs/classes/WorkflowStepOutput.html new file mode 100644 index 0000000..e282e58 --- /dev/null +++ b/docs/classes/WorkflowStepOutput.html @@ -0,0 +1,25 @@ +WorkflowStepOutput | cwl-ts-auto
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Class WorkflowStepOutput

+

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowStepOutput

+

Associate an output parameter of the underlying process with a workflow +parameter. The workflow parameter (given in the id field) be may be used +as a source to connect with input parameters of other workflow steps, or +with an output parameter of the process.

+

A unique identifier for this workflow output parameter. This is +the identifier to use in the source field of WorkflowStepInput +to connect the output value to downstream parameters.

+

Hierarchy

  • Saveable
    • WorkflowStepOutput

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

loadingOptions

loadingOptions: LoadingOptions

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>
  • +

    Used to construct instances of .

    +
    throws

    ValidationException If the document fragment is not a + {@link Dictionary} or validation of fields fails.

    +

    Parameters

    • __doc: any
      +

      Document fragment to load this record object from.

      +
    • baseuri: string
      +

      Base URI to generate child document IDs against.

      +
    • loadingOptions: LoadingOptions
      +

      Context for loading URIs and populating objects.

      +
    • Optional docRoot: string
      +

      ID at this position in the document (if available)

      +

    Returns Promise<Saveable>

    An instance of

    +

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Enumeration Any

Index

Enumeration members

Enumeration members

ANY

ANY = "Any"

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\ No newline at end of file diff --git a/docs/enums/CWLType.html b/docs/enums/CWLType.html new file mode 100644 index 0000000..6f6ac70 --- /dev/null +++ b/docs/enums/CWLType.html @@ -0,0 +1 @@ +CWLType | cwl-ts-auto
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Enumeration CWLType

Index

Enumeration members

Enumeration members

DIRECTORY

DIRECTORY = "Directory"

FILE

FILE = "File"

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\ No newline at end of file diff --git a/docs/enums/CWLVersion.html b/docs/enums/CWLVersion.html new file mode 100644 index 0000000..d127705 --- /dev/null +++ b/docs/enums/CWLVersion.html @@ -0,0 +1 @@ +CWLVersion | cwl-ts-auto
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Enumeration CWLVersion

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Enumeration members

Enumeration members

DRAFT_2

DRAFT_2 = "draft-2"

DRAFT_3

DRAFT_3 = "draft-3"

DRAFT_3_DEV1

DRAFT_3_DEV1 = "draft-3.dev1"

DRAFT_3_DEV2

DRAFT_3_DEV2 = "draft-3.dev2"

DRAFT_3_DEV3

DRAFT_3_DEV3 = "draft-3.dev3"

DRAFT_3_DEV4

DRAFT_3_DEV4 = "draft-3.dev4"

DRAFT_3_DEV5

DRAFT_3_DEV5 = "draft-3.dev5"

DRAFT_4_DEV1

DRAFT_4_DEV1 = "draft-4.dev1"

DRAFT_4_DEV2

DRAFT_4_DEV2 = "draft-4.dev2"

DRAFT_4_DEV3

DRAFT_4_DEV3 = "draft-4.dev3"

V1_0

V1_0 = "v1.0"

V1_0_DEV4

V1_0_DEV4 = "v1.0.dev4"

V1_1

V1_1 = "v1.1"

V1_1_0_DEV1

V1_1_0_DEV1 = "v1.1.0-dev1"

V1_2

V1_2 = "v1.2"

V1_2_0_DEV1

V1_2_0_DEV1 = "v1.2.0-dev1"

V1_2_0_DEV2

V1_2_0_DEV2 = "v1.2.0-dev2"

V1_2_0_DEV3

V1_2_0_DEV3 = "v1.2.0-dev3"

V1_2_0_DEV4

V1_2_0_DEV4 = "v1.2.0-dev4"

V1_2_0_DEV5

V1_2_0_DEV5 = "v1.2.0-dev5"

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\ No newline at end of file diff --git a/docs/enums/CommandLineTool_class.html b/docs/enums/CommandLineTool_class.html new file mode 100644 index 0000000..317a055 --- /dev/null +++ b/docs/enums/CommandLineTool_class.html @@ -0,0 +1 @@ +CommandLineTool_class | cwl-ts-auto
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Enumeration CommandLineTool_class

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COMMANDLINETOOL

COMMANDLINETOOL = "CommandLineTool"

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\ No newline at end of file diff --git a/docs/enums/Directory_class.html b/docs/enums/Directory_class.html new file mode 100644 index 0000000..c88e8fc --- /dev/null +++ b/docs/enums/Directory_class.html @@ -0,0 +1 @@ +Directory_class | cwl-ts-auto
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Enumeration Directory_class

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DIRECTORY

DIRECTORY = "Directory"

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\ No newline at end of file diff --git a/docs/enums/DockerRequirement_class.html b/docs/enums/DockerRequirement_class.html new file mode 100644 index 0000000..2c1e2c6 --- /dev/null +++ b/docs/enums/DockerRequirement_class.html @@ -0,0 +1 @@ +DockerRequirement_class | cwl-ts-auto
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Enumeration DockerRequirement_class

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DOCKERREQUIREMENT

DOCKERREQUIREMENT = "DockerRequirement"

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\ No newline at end of file diff --git a/docs/enums/EnvVarRequirement_class.html b/docs/enums/EnvVarRequirement_class.html new file mode 100644 index 0000000..c516df8 --- /dev/null +++ b/docs/enums/EnvVarRequirement_class.html @@ -0,0 +1 @@ +EnvVarRequirement_class | cwl-ts-auto
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Enumeration EnvVarRequirement_class

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ENVVARREQUIREMENT

ENVVARREQUIREMENT = "EnvVarRequirement"

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\ No newline at end of file diff --git a/docs/enums/Expression.html b/docs/enums/Expression.html new file mode 100644 index 0000000..47e1940 --- /dev/null +++ b/docs/enums/Expression.html @@ -0,0 +1 @@ +Expression | cwl-ts-auto
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Enumeration Expression

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EXPRESSIONPLACEHOLDER

EXPRESSIONPLACEHOLDER = "ExpressionPlaceholder"

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Enumeration ExpressionTool_class

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EXPRESSIONTOOL

EXPRESSIONTOOL = "ExpressionTool"

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\ No newline at end of file diff --git a/docs/enums/File_class.html b/docs/enums/File_class.html new file mode 100644 index 0000000..d99e78a --- /dev/null +++ b/docs/enums/File_class.html @@ -0,0 +1 @@ +File_class | cwl-ts-auto
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Enumeration File_class

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FILE

FILE = "File"

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\ No newline at end of file diff --git a/docs/enums/InitialWorkDirRequirement_class.html b/docs/enums/InitialWorkDirRequirement_class.html new file mode 100644 index 0000000..3d000cf --- /dev/null +++ b/docs/enums/InitialWorkDirRequirement_class.html @@ -0,0 +1 @@ +InitialWorkDirRequirement_class | cwl-ts-auto
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Enumeration InitialWorkDirRequirement_class

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INITIALWORKDIRREQUIREMENT

INITIALWORKDIRREQUIREMENT = "InitialWorkDirRequirement"

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\ No newline at end of file diff --git a/docs/enums/InlineJavascriptRequirement_class.html b/docs/enums/InlineJavascriptRequirement_class.html new file mode 100644 index 0000000..5b5f5b3 --- /dev/null +++ b/docs/enums/InlineJavascriptRequirement_class.html @@ -0,0 +1 @@ +InlineJavascriptRequirement_class | cwl-ts-auto
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Enumeration InlineJavascriptRequirement_class

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INLINEJAVASCRIPTREQUIREMENT

INLINEJAVASCRIPTREQUIREMENT = "InlineJavascriptRequirement"

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\ No newline at end of file diff --git a/docs/enums/InplaceUpdateRequirement_class.html b/docs/enums/InplaceUpdateRequirement_class.html new file mode 100644 index 0000000..0975214 --- /dev/null +++ b/docs/enums/InplaceUpdateRequirement_class.html @@ -0,0 +1 @@ +InplaceUpdateRequirement_class | cwl-ts-auto
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Enumeration InplaceUpdateRequirement_class

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INPLACEUPDATEREQUIREMENT

INPLACEUPDATEREQUIREMENT = "InplaceUpdateRequirement"

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\ No newline at end of file diff --git a/docs/enums/LinkMergeMethod.html b/docs/enums/LinkMergeMethod.html new file mode 100644 index 0000000..3a95775 --- /dev/null +++ b/docs/enums/LinkMergeMethod.html @@ -0,0 +1 @@ +LinkMergeMethod | cwl-ts-auto
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Enumeration LinkMergeMethod

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MERGE_FLATTENED

MERGE_FLATTENED = "merge_flattened"

MERGE_NESTED

MERGE_NESTED = "merge_nested"

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\ No newline at end of file diff --git a/docs/enums/LoadListingEnum.html b/docs/enums/LoadListingEnum.html new file mode 100644 index 0000000..295b25a --- /dev/null +++ b/docs/enums/LoadListingEnum.html @@ -0,0 +1 @@ +LoadListingEnum | cwl-ts-auto
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Enumeration LoadListingEnum

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DEEP_LISTING

DEEP_LISTING = "deep_listing"

NO_LISTING

NO_LISTING = "no_listing"

SHALLOW_LISTING

SHALLOW_LISTING = "shallow_listing"

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\ No newline at end of file diff --git a/docs/enums/LoadListingRequirement_class.html b/docs/enums/LoadListingRequirement_class.html new file mode 100644 index 0000000..7ebf6eb --- /dev/null +++ b/docs/enums/LoadListingRequirement_class.html @@ -0,0 +1 @@ +LoadListingRequirement_class | cwl-ts-auto
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Enumeration LoadListingRequirement_class

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LOADLISTINGREQUIREMENT

LOADLISTINGREQUIREMENT = "LoadListingRequirement"

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\ No newline at end of file diff --git a/docs/enums/MultipleInputFeatureRequirement_class.html b/docs/enums/MultipleInputFeatureRequirement_class.html new file mode 100644 index 0000000..e0317f2 --- /dev/null +++ b/docs/enums/MultipleInputFeatureRequirement_class.html @@ -0,0 +1 @@ +MultipleInputFeatureRequirement_class | cwl-ts-auto
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Enumeration MultipleInputFeatureRequirement_class

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MULTIPLEINPUTFEATUREREQUIREMENT

MULTIPLEINPUTFEATUREREQUIREMENT = "MultipleInputFeatureRequirement"

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\ No newline at end of file diff --git a/docs/enums/NetworkAccess_class.html b/docs/enums/NetworkAccess_class.html new file mode 100644 index 0000000..5424572 --- /dev/null +++ b/docs/enums/NetworkAccess_class.html @@ -0,0 +1 @@ +NetworkAccess_class | cwl-ts-auto
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Enumeration NetworkAccess_class

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NETWORKACCESS

NETWORKACCESS = "NetworkAccess"

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\ No newline at end of file diff --git a/docs/enums/Operation_class.html b/docs/enums/Operation_class.html new file mode 100644 index 0000000..4cb20e3 --- /dev/null +++ b/docs/enums/Operation_class.html @@ -0,0 +1 @@ +Operation_class | cwl-ts-auto
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Enumeration Operation_class

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OPERATION

OPERATION = "Operation"

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\ No newline at end of file diff --git a/docs/enums/PickValueMethod.html b/docs/enums/PickValueMethod.html new file mode 100644 index 0000000..d4165e3 --- /dev/null +++ b/docs/enums/PickValueMethod.html @@ -0,0 +1 @@ +PickValueMethod | cwl-ts-auto
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Enumeration PickValueMethod

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ALL_NON_NULL

ALL_NON_NULL = "all_non_null"

FIRST_NON_NULL

FIRST_NON_NULL = "first_non_null"

THE_ONLY_NON_NULL

THE_ONLY_NON_NULL = "the_only_non_null"

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\ No newline at end of file diff --git a/docs/enums/PrimitiveType.html b/docs/enums/PrimitiveType.html new file mode 100644 index 0000000..03a11f3 --- /dev/null +++ b/docs/enums/PrimitiveType.html @@ -0,0 +1 @@ +PrimitiveType | cwl-ts-auto
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Enumeration PrimitiveType

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BOOLEAN

BOOLEAN = "boolean"

DOUBLE

DOUBLE = "double"

FLOAT

FLOAT = "float"

INT

INT = "int"

LONG

LONG = "long"

NULL

NULL = "null"

STRING

STRING = "string"

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\ No newline at end of file diff --git a/docs/enums/ResourceRequirement_class.html b/docs/enums/ResourceRequirement_class.html new file mode 100644 index 0000000..1e066ab --- /dev/null +++ b/docs/enums/ResourceRequirement_class.html @@ -0,0 +1 @@ +ResourceRequirement_class | cwl-ts-auto
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Enumeration ResourceRequirement_class

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RESOURCEREQUIREMENT

RESOURCEREQUIREMENT = "ResourceRequirement"

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\ No newline at end of file diff --git a/docs/enums/ScatterFeatureRequirement_class.html b/docs/enums/ScatterFeatureRequirement_class.html new file mode 100644 index 0000000..87e319e --- /dev/null +++ b/docs/enums/ScatterFeatureRequirement_class.html @@ -0,0 +1 @@ +ScatterFeatureRequirement_class | cwl-ts-auto
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Enumeration ScatterFeatureRequirement_class

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SCATTERFEATUREREQUIREMENT

SCATTERFEATUREREQUIREMENT = "ScatterFeatureRequirement"

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\ No newline at end of file diff --git a/docs/enums/ScatterMethod.html b/docs/enums/ScatterMethod.html new file mode 100644 index 0000000..7be9c10 --- /dev/null +++ b/docs/enums/ScatterMethod.html @@ -0,0 +1 @@ +ScatterMethod | cwl-ts-auto
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Enumeration ScatterMethod

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Enumeration members

DOTPRODUCT

DOTPRODUCT = "dotproduct"

FLAT_CROSSPRODUCT

FLAT_CROSSPRODUCT = "flat_crossproduct"

NESTED_CROSSPRODUCT

NESTED_CROSSPRODUCT = "nested_crossproduct"

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\ No newline at end of file diff --git a/docs/enums/SchemaDefRequirement_class.html b/docs/enums/SchemaDefRequirement_class.html new file mode 100644 index 0000000..92bdcbb --- /dev/null +++ b/docs/enums/SchemaDefRequirement_class.html @@ -0,0 +1 @@ +SchemaDefRequirement_class | cwl-ts-auto
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Enumeration SchemaDefRequirement_class

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SCHEMADEFREQUIREMENT

SCHEMADEFREQUIREMENT = "SchemaDefRequirement"

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\ No newline at end of file diff --git a/docs/enums/ShellCommandRequirement_class.html b/docs/enums/ShellCommandRequirement_class.html new file mode 100644 index 0000000..55378cf --- /dev/null +++ b/docs/enums/ShellCommandRequirement_class.html @@ -0,0 +1 @@ +ShellCommandRequirement_class | cwl-ts-auto
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Enumeration ShellCommandRequirement_class

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SHELLCOMMANDREQUIREMENT

SHELLCOMMANDREQUIREMENT = "ShellCommandRequirement"

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\ No newline at end of file diff --git a/docs/enums/SoftwareRequirement_class.html b/docs/enums/SoftwareRequirement_class.html new file mode 100644 index 0000000..d3b0d6b --- /dev/null +++ b/docs/enums/SoftwareRequirement_class.html @@ -0,0 +1 @@ +SoftwareRequirement_class | cwl-ts-auto
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Enumeration SoftwareRequirement_class

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SOFTWAREREQUIREMENT

SOFTWAREREQUIREMENT = "SoftwareRequirement"

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\ No newline at end of file diff --git a/docs/enums/StepInputExpressionRequirement_class.html b/docs/enums/StepInputExpressionRequirement_class.html new file mode 100644 index 0000000..6c22839 --- /dev/null +++ b/docs/enums/StepInputExpressionRequirement_class.html @@ -0,0 +1 @@ +StepInputExpressionRequirement_class | cwl-ts-auto
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Enumeration StepInputExpressionRequirement_class

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STEPINPUTEXPRESSIONREQUIREMENT

STEPINPUTEXPRESSIONREQUIREMENT = "StepInputExpressionRequirement"

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\ No newline at end of file diff --git a/docs/enums/SubworkflowFeatureRequirement_class.html b/docs/enums/SubworkflowFeatureRequirement_class.html new file mode 100644 index 0000000..54817d4 --- /dev/null +++ b/docs/enums/SubworkflowFeatureRequirement_class.html @@ -0,0 +1 @@ +SubworkflowFeatureRequirement_class | cwl-ts-auto
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Enumeration SubworkflowFeatureRequirement_class

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SUBWORKFLOWFEATUREREQUIREMENT

SUBWORKFLOWFEATUREREQUIREMENT = "SubworkflowFeatureRequirement"

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\ No newline at end of file diff --git a/docs/enums/ToolTimeLimit_class.html b/docs/enums/ToolTimeLimit_class.html new file mode 100644 index 0000000..d8de880 --- /dev/null +++ b/docs/enums/ToolTimeLimit_class.html @@ -0,0 +1 @@ +ToolTimeLimit_class | cwl-ts-auto
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Enumeration ToolTimeLimit_class

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TOOLTIMELIMIT

TOOLTIMELIMIT = "ToolTimeLimit"

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\ No newline at end of file diff --git a/docs/enums/WorkReuse_class.html b/docs/enums/WorkReuse_class.html new file mode 100644 index 0000000..a3c1ca5 --- /dev/null +++ b/docs/enums/WorkReuse_class.html @@ -0,0 +1 @@ +WorkReuse_class | cwl-ts-auto
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Enumeration WorkReuse_class

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WORKREUSE

WORKREUSE = "WorkReuse"

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\ No newline at end of file diff --git a/docs/enums/Workflow_class.html b/docs/enums/Workflow_class.html new file mode 100644 index 0000000..a35b294 --- /dev/null +++ b/docs/enums/Workflow_class.html @@ -0,0 +1 @@ +Workflow_class | cwl-ts-auto
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Enumeration Workflow_class

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WORKFLOW

WORKFLOW = "Workflow"

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\ No newline at end of file diff --git a/docs/enums/enum_d062602be0b4b8fd33e69e29a841317b6ab665bc.html b/docs/enums/enum_d062602be0b4b8fd33e69e29a841317b6ab665bc.html new file mode 100644 index 0000000..c59cb0c --- /dev/null +++ b/docs/enums/enum_d062602be0b4b8fd33e69e29a841317b6ab665bc.html @@ -0,0 +1 @@ +enum_d062602be0b4b8fd33e69e29a841317b6ab665bc | cwl-ts-auto
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Enumeration enum_d062602be0b4b8fd33e69e29a841317b6ab665bc

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ARRAY

ARRAY = "array"

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\ No newline at end of file diff --git a/docs/enums/enum_d961d79c225752b9fadb617367615ab176b47d77.html b/docs/enums/enum_d961d79c225752b9fadb617367615ab176b47d77.html new file mode 100644 index 0000000..384bdc2 --- /dev/null +++ b/docs/enums/enum_d961d79c225752b9fadb617367615ab176b47d77.html @@ -0,0 +1 @@ +enum_d961d79c225752b9fadb617367615ab176b47d77 | cwl-ts-auto
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Enumeration enum_d961d79c225752b9fadb617367615ab176b47d77

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ENUM

ENUM = "enum"

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\ No newline at end of file diff --git a/docs/enums/enum_d9cba076fca539106791a4f46d198c7fcfbdb779.html b/docs/enums/enum_d9cba076fca539106791a4f46d198c7fcfbdb779.html new file mode 100644 index 0000000..e6c9260 --- /dev/null +++ b/docs/enums/enum_d9cba076fca539106791a4f46d198c7fcfbdb779.html @@ -0,0 +1 @@ +enum_d9cba076fca539106791a4f46d198c7fcfbdb779 | cwl-ts-auto
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Enumeration enum_d9cba076fca539106791a4f46d198c7fcfbdb779

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RECORD

RECORD = "record"

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Enumeration stderr

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Enumeration members

STDERR

STDERR = "stderr"

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Enumeration stdin

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Enumeration members

Enumeration members

STDIN

STDIN = "stdin"

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STDOUT

STDOUT = "stdout"

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cwl-ts-auto

+ +

cwl-ts-auto

+ +

Actions CI +npm version

+

This project contains TypeScript objects and utilities auto-generated by https://github.com/common-workflow-language/schema_salad for parsing documents corresponding to the https://w3id.org/cwl/cwl schema

+ + +

Installation & Usage

+ +

To install the latest version of cwl-ts-auto execute:

+

npm install cwl-ts-auto

+ + +

Loading Documents

+ +

Documents can be loaded by specyfying a file path or by string

+
import * as cwltsauto from 'cwl-ts-auto'
import fs from 'fs'
import url from 'url'

// Load document by file
cwltsauto.loadDocument('./test.cwl')
    .then((file) => {
        if (file instanceof cwltsauto.CommandLineTool) {
            console.log('This document is a CommandLineTool with baseCommand: ', file.baseCommand)
        }
    })
    .catch((e) => {
        if(e instanceof cwltsauto.ValidationException) {
            console.log(e.toString())
        } else {
            console.log(e)
        }
    })

// Load document by string
let docAsString = fs.readFileSync('./test.cwl').toString()
cwltsauto.loadDocumentByString(docAsString, url.pathToFileURL('/your/base/uri/').toString())
    .then((file) => {
        if (file instanceof cwltsauto.CommandLineTool) {
            console.log('This document is a CommandLineTool with baseCommand: ', file.baseCommand)
        }
    })
    .catch((e) => {
        if(e instanceof cwltsauto.ValidationException) {
            console.log(e.toString())
        } else {
            console.log(e)
        }
    })
+
+ + +

Creating, editing and saving Documents

+ +

This example shows how to create a simple CommandLineTool with one input

+
import * as cwltsauto from 'cwl-ts-auto'

let exampleCommandLineTool =
    new cwltsauto.CommandLineTool({
        class_: cwltsauto.CommandLineTool_class.COMMANDLINETOOL,
        inputs: [],
        outputs: []
    })
exampleCommandLineTool.baseCommand = 'echo'

let exampleInput =
    new cwltsauto.CommandInputParameter({
        type: cwltsauto.PrimitiveType.STRING
    })
exampleInput.default_ = 'Hello World!'
exampleCommandLineTool.inputs.push(exampleInput)

console.log(JSON.stringify(exampleCommandLineTool.save()))
+
+ + +

Limitations

+ +

cwl-ts-auto only supports the CWL v1.2 syntax. Other documents have to be upgraded using the cwl-upgrader

+

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Interface ArraySchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/salad#ArraySchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | RecordSchema | EnumSchema | ArraySchema | (string | RecordSchema | EnumSchema | ArraySchema)[]
+

Defines the type of the array elements.

+

type

type: ARRAY
+

Must be array

+

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Interface CommandInputArraySchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputArraySchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

items

items: string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | (string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

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Interface CommandInputEnumSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputEnumSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

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Interface CommandInputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputParameter

+

An input parameter for a CommandLineTool.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turns the input parameters of a process into +command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | (string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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Interface CommandInputRecordFieldProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordField

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

name

name: string
+

The name of the field

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | (string | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

The field type

+

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\ No newline at end of file diff --git a/docs/interfaces/CommandInputRecordSchemaProperties.html b/docs/interfaces/CommandInputRecordSchemaProperties.html new file mode 100644 index 0000000..37a9e15 --- /dev/null +++ b/docs/interfaces/CommandInputRecordSchemaProperties.html @@ -0,0 +1,15 @@ +CommandInputRecordSchemaProperties | cwl-ts-auto
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Interface CommandInputRecordSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputRecordSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: CommandInputRecordField[]
+

Defines the fields of the record.

+

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

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\ No newline at end of file diff --git a/docs/interfaces/CommandInputSchemaProperties.html b/docs/interfaces/CommandInputSchemaProperties.html new file mode 100644 index 0000000..40eba11 --- /dev/null +++ b/docs/interfaces/CommandInputSchemaProperties.html @@ -0,0 +1,3 @@ +CommandInputSchemaProperties | cwl-ts-auto
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Interface CommandInputSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandInputSchema

+

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Interface CommandLineBindableProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBindable

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional inputBinding

inputBinding?: CommandLineBinding
+

Describes how to turn this object into command line arguments.

+

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Interface CommandLineBindingProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineBinding

+

When listed under inputBinding in the input schema, the term +"value" refers to the the corresponding value in the input object. For +binding objects listed in CommandLineTool.arguments, the term "value" +refers to the effective value after evaluating valueFrom.

+

The binding behavior when building the command line depends on the data +type of the value. If there is a mismatch between the type described by +the input schema and the effective value, such as resulting from an +expression evaluation, an implementation must use the data type of the +effective value.

+
    +

  • string: Add prefix and the string to the command line.

    +
    • +

  • number: Add prefix and decimal representation to command line.

    +
    • +

  • boolean: If true, add prefix to the command line. If false, add + nothing.

    +
    • +

  • File: Add prefix and the value of +File.path to the command line.

    +
    • +

  • Directory: Add prefix and the value of +Directory.path to the command line.

    +
    • +

  • array: If itemSeparator is specified, add prefix and the join + the array into a single string with itemSeparator separating the + items. Otherwise first add prefix, then recursively process + individual elements. + If the array is empty, it does not add anything to command line.

    +
    • +

  • object: Add prefix only, and recursively add object fields for + which inputBinding is specified.

    +
    • +

  • null: Add nothing.

    +
    • +
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional itemSeparator

itemSeparator?: string
+

Join the array elements into a single string with the elements +separated by by itemSeparator.

+

Optional loadContents

loadContents?: boolean
+

Use of loadContents in InputBinding is deprecated. +Preserved for v1.0 backwards compatability. Will be removed in +CWL v2.0. Use InputParameter.loadContents instead.

+

Optional position

position?: string | number
+

The sorting key. Default position is 0. If a CWL Parameter Reference +or CWL Expression is used and if the +inputBinding is associated with an input parameter, then the value of +self will be the value of the input parameter. Input parameter +defaults (as specified by the InputParameter.default field) must be +applied before evaluating the expression. Expressions must return a +single value of type int or a null.

+

Optional prefix

prefix?: string
+

Command line prefix to add before the value.

+

Optional separate

separate?: boolean
+

If true (default), then the prefix and value must be added as separate +command line arguments; if false, prefix and value must be concatenated +into a single command line argument.

+

Optional shellQuote

shellQuote?: boolean
+

If ShellCommandRequirement is in the requirements for the current command, +this controls whether the value is quoted on the command line (default is true). +Use shellQuote: false to inject metacharacters for operations such as pipes.

+

If shellQuote is true or not provided, the implementation must not +permit interpretation of any shell metacharacters or directives.

+

Optional valueFrom

valueFrom?: string
+

If valueFrom is a constant string value, use this as the value and +apply the binding rules above.

+

If valueFrom is an expression, evaluate the expression to yield the +actual value to use to build the command line and apply the binding +rules above. If the inputBinding is associated with an input +parameter, the value of self in the expression will be the value of +the input parameter. Input parameter defaults (as specified by the +InputParameter.default field) must be applied before evaluating the +expression.

+

If the value of the associated input parameter is null, valueFrom is +not evaluated and nothing is added to the command line.

+

When a binding is part of the CommandLineTool.arguments field, +the valueFrom field is required.

+

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Interface CommandLineToolProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandLineTool

+

This defines the schema of the CWL Command Line Tool Description document.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional arguments_

arguments_?: (string | CommandLineBinding)[]
+

Command line bindings which are not directly associated with input +parameters. If the value is a string, it is used as a string literal +argument. If it is an Expression, the result of the evaluation is used +as an argument.

+

Optional baseCommand

baseCommand?: string | string[]
+

Specifies the program to execute. If an array, the first element of +the array is the command to execute, and subsequent elements are +mandatory command line arguments. The elements in baseCommand must +appear before any command line bindings from inputBinding or +arguments.

+

If baseCommand is not provided or is an empty array, the first +element of the command line produced after processing inputBinding or +arguments must be used as the program to execute.

+

If the program includes a path separator character it must +be an absolute path, otherwise it is an error. If the program does not +include a path separator, search the $PATH variable in the runtime +environment of the workflow runner find the absolute path of the +executable.

+

class_

class_: COMMANDLINETOOL

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: CommandInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

outputs

outputs: CommandOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional permanentFailCodes

permanentFailCodes?: number[]
+

Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. +If not specified, all exit codes except 0 are considered permanent failure.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

Optional stderr

stderr?: string
+

Capture the command's standard error stream to a file written to +the designated output directory.

+

If stderr is a string, it specifies the file name to use.

+

If stderr is an expression, the expression is evaluated and must +return a string with the file name to use to capture stderr. If the +return value is not a string, or the resulting path contains illegal +characters (such as the path separator /) it is an error.

+

Optional stdin

stdin?: string
+

A path to a file whose contents must be piped into the command's +standard input stream.

+

Optional stdout

stdout?: string
+

Capture the command's standard output stream to a file written to +the designated output directory.

+

If stdout is a string, it specifies the file name to use.

+

If stdout is an expression, the expression is evaluated and must +return a string with the file name to use to capture stdout. If the +return value is not a string, or the resulting path contains illegal +characters (such as the path separator /) it is an error.

+

Optional successCodes

successCodes?: number[]
+

Exit codes that indicate the process completed successfully.

+

If not specified, only exit code 0 is considered success.

+

Optional temporaryFailCodes

temporaryFailCodes?: number[]
+

Exit codes that indicate the process failed due to a possibly +temporary condition, where executing the process with the same +runtime environment and inputs may produce different results.

+

If not specified, no exit codes are considered temporary failure.

+

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Interface CommandOutputArraySchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputArraySchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema | (string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

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Interface CommandOutputBindingProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputBinding

+

Describes how to generate an output parameter based on the files produced +by a CommandLineTool.

+

The output parameter value is generated by applying these operations in the +following order:

+
    +
  • glob
    • +
  • loadContents
    • +
  • outputEval
    • +
  • secondaryFiles
    • +
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional glob

glob?: string | string[]
+

Find files or directories relative to the output directory, using POSIX +glob(3) pathname matching. If an array is provided, find files or +directories that match any pattern in the array. If an expression is +provided, the expression must return a string or an array of strings, +which will then be evaluated as one or more glob patterns. Must only +match and return files/directories which actually exist.

+

If the value of glob is a relative path pattern (does not +begin with a slash '/') then it is resolved relative to the +output directory. If the value of the glob is an absolute +path pattern (it does begin with a slash '/') then it must +refer to a path within the output directory. It is an error +if any glob resolves to a path outside the output directory. +Specifically this means globs that resolve to paths outside the output +directory are illegal.

+

A glob may match a path within the output directory which is +actually a symlink to another file. In this case, the +expected behavior is for the resulting File/Directory object to take the +basename (and corresponding nameroot and nameext) of the +symlink. The location of the File/Directory is implementation +dependent, but logically the File/Directory should have the same content +as the symlink target. Platforms may stage output files/directories to +cloud storage that lack the concept of a symlink. In +this case file content and directories may be duplicated, or (to avoid +duplication) the File/Directory location may refer to the symlink +target.

+

It is an error if a symlink in the output directory (or any +symlink in a chain of links) refers to any file or directory +that is not under an input or output directory.

+

Implementations may shut down a container before globbing +output, so globs and expressions must not assume access to the +container filesystem except for declared input and output.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

Optional outputEval

outputEval?: string
+

Evaluate an expression to generate the output value. If +glob was specified, the value of self must be an array +containing file objects that were matched. If no files were +matched, self must be a zero length array; if a single file +was matched, the value of self is an array of a single +element. The exit code of the process is +available in the expression as runtime.exitCode.

+

Additionally if loadContents is true, the file must be a +UTF-8 text file 64 KiB or smaller, and the implementation must +read the entire contents of the file (or file array) and place +it in the contents field of the File object for use in +outputEval. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

If a tool needs to return a large amount of structured data to +the workflow, loading the output object from cwl.output.json +bypasses outputEval and is not subject to the 64 KiB +loadContents limit.

+

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Interface CommandOutputEnumSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputEnumSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

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Interface CommandOutputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputParameter

+

An output parameter for a CommandLineTool.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional outputBinding

outputBinding?: CommandOutputBinding
+

Describes how to generate this output object based on the files produced by a CommandLineTool

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema | (string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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Interface CommandOutputRecordFieldProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordField

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

name

name: string
+

The name of the field

+

Optional outputBinding

outputBinding?: CommandOutputBinding
+

Describes how to generate this output object based on the files +produced by a CommandLineTool

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema | (string | CommandOutputRecordSchema | CommandOutputEnumSchema | CommandOutputArraySchema)[]
+

The field type

+

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Interface CommandOutputRecordSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#CommandOutputRecordSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: CommandOutputRecordField[]
+

Defines the fields of the record.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

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Interface DirectoryProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Directory

+

Represents a directory to present to a command line tool.

+

Directories are represented as objects with class of Directory. Directory objects have +a number of properties that provide metadata about the directory.

+

The location property of a Directory is a URI that uniquely identifies +the directory. Implementations must support the file:// URI scheme and may +support other schemes such as http://. Alternately to location, +implementations must also accept the path property on Directory, which +must be a filesystem path available on the same host as the CWL runner (for +inputs) or the runtime environment of a command line tool execution (for +command line tool outputs).

+

A Directory object may have a listing field. This is a list of File and +Directory objects that are contained in the Directory. For each entry in +listing, the basename property defines the name of the File or +Subdirectory when staged to disk. If listing is not provided, the +implementation must have some way of fetching the Directory listing at +runtime based on the location field.

+

If a Directory does not have location, it is a Directory literal. A +Directory literal must provide listing. Directory literals must be +created on disk at runtime as needed.

+

The resources in a Directory literal do not need to have any implied +relationship in their location. For example, a Directory listing may +contain two files located on different hosts. It is the responsibility of +the runtime to ensure that those files are staged to disk appropriately. +Secondary files associated with files in listing must also be staged to +the same Directory.

+

When executing a CommandLineTool, Directories must be recursively staged +first and have local values of path assigend.

+

Directory objects in CommandLineTool output must provide either a +location URI or a path property in the context of the tool execution +runtime (local to the compute node, or within the executing container).

+

An ExpressionTool may forward file references from input to output by using +the same value for location.

+

Name conflicts (the same basename appearing multiple times in listing +or in any entry in secondaryFiles in the listing) is a fatal error.

+

Hierarchy

  • DirectoryProperties

Implemented by

Index

Properties

Properties

Optional basename

basename?: string
+

The base name of the directory, that is, the name of the file without any +leading directory path. The base name must not contain a slash /.

+

If not provided, the implementation must set this field based on the +location field by taking the final path component after parsing +location as an IRI. If basename is provided, it is not required to +match the value from location.

+

When this file is made available to a CommandLineTool, it must be named +with basename, i.e. the final component of the path field must match +basename.

+

class_

class_: DIRECTORY
+

Must be Directory to indicate this object describes a Directory.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional listing

listing?: (File | Directory)[]
+

List of files or subdirectories contained in this directory. The name +of each file or subdirectory is determined by the basename field of +each File or Directory object. It is an error if a File shares a +basename with any other entry in listing. If two or more +Directory object share the same basename, this must be treated as +equivalent to a single subdirectory with the listings recursively +merged.

+

Optional location

location?: string
+

An IRI that identifies the directory resource. This may be a relative +reference, in which case it must be resolved using the base IRI of the +document. The location may refer to a local or remote resource. If +the listing field is not set, the implementation must use the +location IRI to retrieve directory listing. If an implementation is +unable to retrieve the directory listing stored at a remote resource (due to +unsupported protocol, access denied, or other issue) it must signal an +error.

+

If the location field is not provided, the listing field must be +provided. The implementation must assign a unique identifier for +the location field.

+

If the path field is provided but the location field is not, an +implementation may assign the value of the path field to location, +then follow the rules above.

+

Optional path

path?: string
+

The local path where the Directory is made available prior to executing a +CommandLineTool. This must be set by the implementation. This field +must not be used in any other context. The command line tool being +executed must be able to to access the directory at path using the POSIX +opendir(2) syscall.

+

If the path contains POSIX shell metacharacters +(|,&, ;, <, >, (,), $,`, \, ", ', +<space>, <tab>, and <newline>) or characters +not allowed +for Internationalized Domain Names for Applications +then implementations may terminate the process with a +permanentFailure.

+

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Interface DirentProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Dirent

+

Define a file or subdirectory that must be staged to a particular +place prior to executing the command line tool. May be the result +of executing an expression, such as building a configuration file +from a template.

+

Usually files are staged within the designated output directory. +However, under certain circumstances, files may be staged at +arbitrary locations, see discussion for entryname.

+

Hierarchy

  • DirentProperties

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Properties

Properties

entry

entry: string
+

If the value is a string literal or an expression which evaluates to a +string, a new text file must be created with the string as the file contents.

+

If the value is an expression that evaluates to a File or +Directory object, or an array of File or Directory +objects, this indicates the referenced file or directory +should be added to the designated output directory prior to +executing the tool.

+

If the value is an expression that evaluates to null, +nothing is added to the designated output directory, the entry +has no effect.

+

If the value is an expression that evaluates to some other +array, number, or object not consisting of File or +Directory objects, a new file must be created with the value +serialized to JSON text as the file contents. The JSON +serialization behavior should match the behavior of string +interpolation of Parameter +references.

+

Optional entryname

entryname?: string
+

The "target" name of the file or subdirectory. If entry is +a File or Directory, the entryname field overrides the value +of basename of the File or Directory object.

+
    +
  • Required when entry evaluates to file contents only
    • +
  • Optional when entry evaluates to a File or Directory object with a basename
    • +
  • Invalid when entry evaluates to an array of File or Directory objects.
    • +
+

If entryname is a relative path, it specifies a name within +the designated output directory. A relative path starting +with ../ or that resolves to location above the designated output directory is an error.

+

If entryname is an absolute path (starts with a slash /) +it is an error unless the following conditions are met:

+
    +
  • DockerRequirement is present in requirements
    • +
  • The program is will run inside a software container + where, from the perspective of the program, the root + filesystem is not shared with any other user or + running program.
    • +
+

In this case, and the above conditions are met, then +entryname may specify the absolute path within the container +where the file or directory must be placed.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional writable

writable?: boolean
+

If true, the File or Directory (or array of Files or +Directories) declared in entry must be writable by the tool.

+

Changes to the file or directory must be isolated and not +visible by any other CommandLineTool process. This may be +implemented by making a copy of the original file or +directory.

+

Disruptive changes to the referenced file or directory must not +be allowed unless InplaceUpdateRequirement.inplaceUpdate is true.

+

Default false (files and directories read-only by default).

+

A directory marked as writable: true implies that all files and +subdirectories are recursively writable as well.

+

If writable is false, the file may be made available using a +bind mount or file system link to avoid unnecessary copying of +the input file. Command line tools may receive an error on +attempting to rename or delete files or directories that are +not explicitly marked as writable.

+

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Interface DockerRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#DockerRequirement

+

Indicates that a workflow component should be run in a +Docker or Docker-compatible (such as +Singularity and udocker) container environment and +specifies how to fetch or build the image.

+

If a CommandLineTool lists DockerRequirement under +hints (or requirements), it may (or must) be run in the specified Docker +container.

+

The platform must first acquire or install the correct Docker image as +specified by dockerPull, dockerImport, dockerLoad or dockerFile.

+

The platform must execute the tool in the container using docker run with +the appropriate Docker image and tool command line.

+

The workflow platform may provide input files and the designated output +directory through the use of volume bind mounts. The platform should rewrite +file paths in the input object to correspond to the Docker bind mounted +locations. That is, the platform should rewrite values in the parameter context +such as runtime.outdir, runtime.tmpdir and others to be valid paths +within the container. The platform must ensure that runtime.outdir and +runtime.tmpdir are distinct directories.

+

When running a tool contained in Docker, the workflow platform must not +assume anything about the contents of the Docker container, such as the +presence or absence of specific software, except to assume that the +generated command line represents a valid command within the runtime +environment of the container.

+

A container image may specify an +ENTRYPOINT +and/or +CMD. +Command line arguments will be appended after all elements of +ENTRYPOINT, and will override all elements specified using CMD (in +other words, CMD is only used when the CommandLineTool definition +produces an empty command line).

+

Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility +concerns of the implicit hidden execution point (For further discussion, see +https://doi.org/10.12688/f1000research.15140.1). Portable +CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. +CommandLineTools which do rely on ENTRYPOINT or CMD must list DockerRequirement in the +requirements section.

+ + +

Interaction with other requirements

+ +

If EnvVarRequirement is specified alongside a +DockerRequirement, the environment variables must be provided to Docker +using --env or --env-file and interact with the container's preexisting +environment as defined by Docker.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: DOCKERREQUIREMENT
+

Always 'DockerRequirement'

+

Optional dockerFile

dockerFile?: string
+

Supply the contents of a Dockerfile which will be built using docker build.

+

Optional dockerImageId

dockerImageId?: string
+

The image id that will be used for docker run. May be a +human-readable image name or the image identifier hash. May be skipped +if dockerPull is specified, in which case the dockerPull image id +must be used.

+

Optional dockerImport

dockerImport?: string
+

Provide HTTP URL to download and gunzip a Docker images using `docker import.

+

Optional dockerLoad

dockerLoad?: string
+

Specify a HTTP URL from which to download a Docker image using docker load.

+

Optional dockerOutputDirectory

dockerOutputDirectory?: string
+

Set the designated output directory to a specific location inside the +Docker container.

+

Optional dockerPull

dockerPull?: string
+

Specify a Docker image to retrieve using docker pull. Can contain the +immutable digest to ensure an exact container is used: +dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface DocumentedProperties

+

Auto-generated interface for https://w3id.org/cwl/salad#Documented

+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

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Interface EnumSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/salad#EnumSchema

+

Define an enumerated type.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

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Interface EnvVarRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#EnvVarRequirement

+

Define a list of environment variables which will be set in the +execution environment of the tool. See EnvironmentDef for details.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: ENVVARREQUIREMENT
+

Always 'EnvVarRequirement'

+

envDef

envDef: EnvironmentDef[]
+

The list of environment variables.

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface EnvironmentDefProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#EnvironmentDef

+

Define an environment variable that will be set in the runtime environment +by the workflow platform when executing the command line tool. May be the +result of executing an expression, such as getting a parameter from input.

+

Hierarchy

  • EnvironmentDefProperties

Implemented by

Index

Properties

Properties

envName

envName: string
+

The environment variable name

+

envValue

envValue: string
+

The environment variable value

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface ExpressionToolOutputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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Interface ExpressionToolProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ExpressionTool

+

An ExpressionTool is a type of Process object that can be run by itself +or as a Workflow step. It executes a pure Javascript expression that has +access to the same input parameters as a workflow. It is meant to be used +sparingly as a way to isolate complex Javascript expressions that need to +operate on input data and produce some result; perhaps just a +rearrangement of the inputs. No Docker software container is required +or allowed.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: EXPRESSIONTOOL

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

expression

expression: string
+

The expression to execute. The expression must return a plain +Javascript object which matches the output parameters of the +ExpressionTool.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: WorkflowInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

outputs

outputs: ExpressionToolOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

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Interface FieldBaseProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#FieldBase

+

Hierarchy

Index

Properties

Properties

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

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Interface FileProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#File

+

Represents a file (or group of files when secondaryFiles is provided) that +will be accessible by tools using standard POSIX file system call API such as +open(2) and read(2).

+

Files are represented as objects with class of File. File objects have +a number of properties that provide metadata about the file.

+

The location property of a File is a URI that uniquely identifies the +file. Implementations must support the file:// URI scheme and may support +other schemes such as http://. The value of location may also be a +relative reference, in which case it must be resolved relative to the URI +of the document it appears in. Alternately to location, implementations +must also accept the path property on File, which must be a filesystem +path available on the same host as the CWL runner (for inputs) or the +runtime environment of a command line tool execution (for command line tool +outputs).

+

If no location or path is specified, a file object must specify +contents with the UTF-8 text content of the file. This is a "file +literal". File literals do not correspond to external resources, but are +created on disk with contents with when needed for a executing a tool. +Where appropriate, expressions can return file literals to define new files +on a runtime. The maximum size of contents is 64 kilobytes.

+

The basename property defines the filename on disk where the file is +staged. This may differ from the resource name. If not provided, +basename must be computed from the last path part of location and made +available to expressions.

+

The secondaryFiles property is a list of File or Directory objects that +must be staged in the same directory as the primary file. It is an error +for file names to be duplicated in secondaryFiles.

+

The size property is the size in bytes of the File. It must be computed +from the resource and made available to expressions. The checksum field +contains a cryptographic hash of the file content for use it verifying file +contents. Implementations may, at user option, enable or disable +computation of the checksum field for performance or other reasons. +However, the ability to compute output checksums is required to pass the +CWL conformance test suite.

+

When executing a CommandLineTool, the files and secondary files may be +staged to an arbitrary directory, but must use the value of basename for +the filename. The path property must be file path in the context of the +tool execution runtime (local to the compute node, or within the executing +container). All computed properties should be available to expressions. +File literals also must be staged and path must be set.

+

When collecting CommandLineTool outputs, glob matching returns file paths +(with the path property) and the derived properties. This can all be +modified by outputEval. Alternately, if the file cwl.output.json is +present in the output, outputBinding is ignored.

+

File objects in the output must provide either a location URI or a path +property in the context of the tool execution runtime (local to the compute +node, or within the executing container).

+

When evaluating an ExpressionTool, file objects must be referenced via +location (the expression tool does not have access to files on disk so +path is meaningless) or as file literals. It is legal to return a file +object with an existing location but a different basename. The +loadContents field of ExpressionTool inputs behaves the same as on +CommandLineTool inputs, however it is not meaningful on the outputs.

+

An ExpressionTool may forward file references from input to output by using +the same value for location.

+

Hierarchy

  • FileProperties

Implemented by

Index

Properties

Properties

Optional basename

basename?: string
+

The base name of the file, that is, the name of the file without any +leading directory path. The base name must not contain a slash /.

+

If not provided, the implementation must set this field based on the +location field by taking the final path component after parsing +location as an IRI. If basename is provided, it is not required to +match the value from location.

+

When this file is made available to a CommandLineTool, it must be named +with basename, i.e. the final component of the path field must match +basename.

+

Optional checksum

checksum?: string
+

Optional hash code for validating file integrity. Currently must be in the form +"sha1$ + hexadecimal string" using the SHA-1 algorithm.

+

class_

class_: FILE
+

Must be File to indicate this object describes a file.

+

Optional contents

contents?: string
+

File contents literal.

+

If neither location nor path is provided, contents must be +non-null. The implementation must assign a unique identifier for the +location field. When the file is staged as input to CommandLineTool, +the value of contents must be written to a file.

+

If contents is set as a result of an Javascript expression, +an entry in InitialWorkDirRequirement, or read in from +cwl.output.json, there is no specified upper limit on the +size of contents. Implementations may have practical limits +on the size of contents based on memory and storage +available to the workflow runner or other factors.

+

If the loadContents field of an InputParameter or +OutputParameter is true, and the input or output File object +location is valid, the file must be a UTF-8 text file 64 KiB +or smaller, and the implementation must read the entire +contents of the file and place it in the contents field. If +the size of the file is greater than 64 KiB, the +implementation must raise a fatal error.

+

Optional dirname

dirname?: string
+

The name of the directory containing file, that is, the path leading up +to the final slash in the path such that dirname + '/' + basename == path.

+

The implementation must set this field based on the value of path +prior to evaluating parameter references or expressions in a +CommandLineTool document. This field must not be used in any other +context.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

The format of the file: this must be an IRI of a concept node that +represents the file format, preferrably defined within an ontology. +If no ontology is available, file formats may be tested by exact match.

+

Reasoning about format compatability must be done by checking that an +input file format is the same, owl:equivalentClass or +rdfs:subClassOf the format required by the input parameter. +owl:equivalentClass is transitive with rdfs:subClassOf, e.g. if +<B> owl:equivalentClass <C> and <B> owl:subclassOf <A> then infer +<C> owl:subclassOf <A>.

+

File format ontologies may be provided in the "$schemas" metadata at the +root of the document. If no ontologies are specified in $schemas, the +runtime may perform exact file format matches.

+

Optional location

location?: string
+

An IRI that identifies the file resource. This may be a relative +reference, in which case it must be resolved using the base IRI of the +document. The location may refer to a local or remote resource; the +implementation must use the IRI to retrieve file content. If an +implementation is unable to retrieve the file content stored at a +remote resource (due to unsupported protocol, access denied, or other +issue) it must signal an error.

+

If the location field is not provided, the contents field must be +provided. The implementation must assign a unique identifier for +the location field.

+

If the path field is provided but the location field is not, an +implementation may assign the value of the path field to location, +then follow the rules above.

+

Optional nameext

nameext?: string
+

The basename extension such that nameroot + nameext == basename, and +nameext is empty or begins with a period and contains at most one +period. Leading periods on the basename are ignored; a basename of +.cshrc will have an empty nameext.

+

The implementation must set this field automatically based on the value +of basename prior to evaluating parameter references or expressions.

+

Optional nameroot

nameroot?: string
+

The basename root such that nameroot + nameext == basename, and +nameext is empty or begins with a period and contains at most one +period. For the purposess of path splitting leading periods on the +basename are ignored; a basename of .cshrc will have a nameroot of +.cshrc.

+

The implementation must set this field automatically based on the value +of basename prior to evaluating parameter references or expressions.

+

Optional path

path?: string
+

The local host path where the File is available when a CommandLineTool is +executed. This field must be set by the implementation. The final +path component must match the value of basename. This field +must not be used in any other context. The command line tool being +executed must be able to to access the file at path using the POSIX +open(2) syscall.

+

As a special case, if the path field is provided but the location +field is not, an implementation may assign the value of the path +field to location, and remove the path field.

+

If the path contains POSIX shell metacharacters +(|,&, ;, <, >, (,), $,`, \, ", ', +<space>, <tab>, and <newline>) or characters +not allowed +for Internationalized Domain Names for Applications +then implementations may terminate the process with a +permanentFailure.

+

Optional secondaryFiles

secondaryFiles?: (File | Directory)[]
+

A list of additional files or directories that are associated with the +primary file and must be transferred alongside the primary file. +Examples include indexes of the primary file, or external references +which must be included when loading primary document. A file object +listed in secondaryFiles may itself include secondaryFiles for +which the same rules apply.

+

Optional size

size?: number
+

Optional file size (in bytes)

+

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Interface IOSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#IOSchema

+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

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\ No newline at end of file diff --git a/docs/interfaces/IdentifiedProperties.html b/docs/interfaces/IdentifiedProperties.html new file mode 100644 index 0000000..573d5d2 --- /dev/null +++ b/docs/interfaces/IdentifiedProperties.html @@ -0,0 +1,5 @@ +IdentifiedProperties | cwl-ts-auto
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Interface IdentifiedProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Identified

+

Hierarchy

Index

Properties

Properties

Optional id

id?: string
+

The unique identifier for this object.

+

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\ No newline at end of file diff --git a/docs/interfaces/InitialWorkDirRequirementProperties.html b/docs/interfaces/InitialWorkDirRequirementProperties.html new file mode 100644 index 0000000..376c7f9 --- /dev/null +++ b/docs/interfaces/InitialWorkDirRequirementProperties.html @@ -0,0 +1,25 @@ +InitialWorkDirRequirementProperties | cwl-ts-auto
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Interface InitialWorkDirRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InitialWorkDirRequirement

+

Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool. +Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for Dirent.entryname. Together with DockerRequirement.dockerOutputDirectory this it possible to control the locations of both input and output files when running in containers.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: INITIALWORKDIRREQUIREMENT
+

InitialWorkDirRequirement

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional listing

listing?: string | (undefined | string | File | Directory | (File | Directory)[] | Dirent)[]
+

The list of files or subdirectories that must be staged prior +to executing the command line tool.

+

Return type of each expression must validate as ["null", File, Directory, Dirent, {type: array, items: [File, Directory]}].

+

Each File or Directory that is returned by an Expression +must be added to the designated output directory prior to +executing the tool.

+

Each Dirent record that is listed or returned by an +expression specifies a file to be created or staged in the +designated output directory prior to executing the tool.

+

Expressions may return null, in which case they have no effect.

+

Files or Directories which are listed in the input parameters +and appear in the InitialWorkDirRequirement listing must +have their path set to their staged location. If the same +File or Directory appears more than once in the +InitialWorkDirRequirement listing, the implementation must +choose exactly one value for path; how this value is chosen +is undefined.

+

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\ No newline at end of file diff --git a/docs/interfaces/InlineJavascriptRequirementProperties.html b/docs/interfaces/InlineJavascriptRequirementProperties.html new file mode 100644 index 0000000..e110844 --- /dev/null +++ b/docs/interfaces/InlineJavascriptRequirementProperties.html @@ -0,0 +1,12 @@ +InlineJavascriptRequirementProperties | cwl-ts-auto
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Interface InlineJavascriptRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InlineJavascriptRequirement

+

Indicates that the workflow platform must support inline Javascript expressions. +If this requirement is not present, the workflow platform must not perform expression +interpolatation.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: INLINEJAVASCRIPTREQUIREMENT
+

Always 'InlineJavascriptRequirement'

+

Optional expressionLib

expressionLib?: string[]
+

Additional code fragments that will also be inserted +before executing the expression code. Allows for function definitions that may +be called from CWL expressions.

+

Optional extensionFields

extensionFields?: Dictionary<any>

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\ No newline at end of file diff --git a/docs/interfaces/InplaceUpdateRequirementProperties.html b/docs/interfaces/InplaceUpdateRequirementProperties.html new file mode 100644 index 0000000..0626980 --- /dev/null +++ b/docs/interfaces/InplaceUpdateRequirementProperties.html @@ -0,0 +1,29 @@ +InplaceUpdateRequirementProperties | cwl-ts-auto
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Interface InplaceUpdateRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InplaceUpdateRequirement

+

If inplaceUpdate is true, then an implementation supporting this +feature may permit tools to directly update files with writable: true in InitialWorkDirRequirement. That is, as an optimization, +files may be destructively modified in place as opposed to copied +and updated.

+

An implementation must ensure that only one workflow step may +access a writable file at a time. It is an error if a file which +is writable by one workflow step file is accessed (for reading or +writing) by any other workflow step running independently. +However, a file which has been updated in a previous completed +step may be used as input to multiple steps, provided it is +read-only in every step.

+

Workflow steps which modify a file must produce the modified file +as output. Downstream steps which futher process the file must +use the output of previous steps, and not refer to a common input +(this is necessary for both ordering and correctness).

+

Workflow authors should provide this in the hints section. The +intent of this feature is that workflows produce the same results +whether or not InplaceUpdateRequirement is supported by the +implementation, and this feature is primarily available as an +optimization for particular environments.

+

Users and implementers should be aware that workflows that +destructively modify inputs may not be repeatable or reproducible. +In particular, enabling this feature implies that WorkReuse should +not be enabled.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: INPLACEUPDATEREQUIREMENT
+

Always 'InplaceUpdateRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

inplaceUpdate

inplaceUpdate: boolean

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Interface InputArraySchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputArraySchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

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\ No newline at end of file diff --git a/docs/interfaces/InputBindingProperties.html b/docs/interfaces/InputBindingProperties.html new file mode 100644 index 0000000..e103844 --- /dev/null +++ b/docs/interfaces/InputBindingProperties.html @@ -0,0 +1,7 @@ +InputBindingProperties | cwl-ts-auto
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Interface InputBindingProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputBinding

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional loadContents

loadContents?: boolean
+

Use of loadContents in InputBinding is deprecated. +Preserved for v1.0 backwards compatability. Will be removed in +CWL v2.0. Use InputParameter.loadContents instead.

+

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\ No newline at end of file diff --git a/docs/interfaces/InputEnumSchemaProperties.html b/docs/interfaces/InputEnumSchemaProperties.html new file mode 100644 index 0000000..ab5ce03 --- /dev/null +++ b/docs/interfaces/InputEnumSchemaProperties.html @@ -0,0 +1,13 @@ +InputEnumSchemaProperties | cwl-ts-auto
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Interface InputEnumSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputEnumSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

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\ No newline at end of file diff --git a/docs/interfaces/InputFormatProperties.html b/docs/interfaces/InputFormatProperties.html new file mode 100644 index 0000000..bc49a26 --- /dev/null +++ b/docs/interfaces/InputFormatProperties.html @@ -0,0 +1,9 @@ +InputFormatProperties | cwl-ts-auto
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Interface InputFormatProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputFormat

+

Hierarchy

Index

Properties

Properties

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

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\ No newline at end of file diff --git a/docs/interfaces/InputParameterProperties.html b/docs/interfaces/InputParameterProperties.html new file mode 100644 index 0000000..6c7c1b6 --- /dev/null +++ b/docs/interfaces/InputParameterProperties.html @@ -0,0 +1,83 @@ +InputParameterProperties | cwl-ts-auto
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Interface InputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter

+

Hierarchy

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

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\ No newline at end of file diff --git a/docs/interfaces/InputRecordFieldProperties.html b/docs/interfaces/InputRecordFieldProperties.html new file mode 100644 index 0000000..a333d9e --- /dev/null +++ b/docs/interfaces/InputRecordFieldProperties.html @@ -0,0 +1,80 @@ +InputRecordFieldProperties | cwl-ts-auto
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Interface InputRecordFieldProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordField

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

name

name: string
+

The name of the field

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

The field type

+

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\ No newline at end of file diff --git a/docs/interfaces/InputRecordSchemaProperties.html b/docs/interfaces/InputRecordSchemaProperties.html new file mode 100644 index 0000000..d9eb648 --- /dev/null +++ b/docs/interfaces/InputRecordSchemaProperties.html @@ -0,0 +1,13 @@ +InputRecordSchemaProperties | cwl-ts-auto
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Interface InputRecordSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputRecordSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: InputRecordField[]
+

Defines the fields of the record.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

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\ No newline at end of file diff --git a/docs/interfaces/InputSchemaProperties.html b/docs/interfaces/InputSchemaProperties.html new file mode 100644 index 0000000..62418d1 --- /dev/null +++ b/docs/interfaces/InputSchemaProperties.html @@ -0,0 +1,9 @@ +InputSchemaProperties | cwl-ts-auto
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Interface InputSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#InputSchema

+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

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\ No newline at end of file diff --git a/docs/interfaces/LabeledProperties.html b/docs/interfaces/LabeledProperties.html new file mode 100644 index 0000000..cebd7ee --- /dev/null +++ b/docs/interfaces/LabeledProperties.html @@ -0,0 +1,5 @@ +LabeledProperties | cwl-ts-auto
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Interface LabeledProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Labeled

+

Hierarchy

Index

Properties

Properties

Optional label

label?: string
+

A short, human-readable label of this object.

+

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\ No newline at end of file diff --git a/docs/interfaces/LoadContentsProperties.html b/docs/interfaces/LoadContentsProperties.html new file mode 100644 index 0000000..3c818a2 --- /dev/null +++ b/docs/interfaces/LoadContentsProperties.html @@ -0,0 +1,21 @@ +LoadContentsProperties | cwl-ts-auto
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Interface LoadContentsProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#LoadContents

+

Hierarchy

Index

Properties

Properties

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

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\ No newline at end of file diff --git a/docs/interfaces/LoadListingRequirementProperties.html b/docs/interfaces/LoadListingRequirementProperties.html new file mode 100644 index 0000000..67f4458 --- /dev/null +++ b/docs/interfaces/LoadListingRequirementProperties.html @@ -0,0 +1,7 @@ +LoadListingRequirementProperties | cwl-ts-auto
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Interface LoadListingRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#LoadListingRequirement

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: LOADLISTINGREQUIREMENT
+

Always 'LoadListingRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional loadListing

loadListing?: LoadListingEnum

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\ No newline at end of file diff --git a/docs/interfaces/MultipleInputFeatureRequirementProperties.html b/docs/interfaces/MultipleInputFeatureRequirementProperties.html new file mode 100644 index 0000000..d81c27e --- /dev/null +++ b/docs/interfaces/MultipleInputFeatureRequirementProperties.html @@ -0,0 +1,7 @@ +MultipleInputFeatureRequirementProperties | cwl-ts-auto
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Interface MultipleInputFeatureRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement

+

Indicates that the workflow platform must support multiple inbound data links +listed in the source field of WorkflowStepInput.

+

Hierarchy

Implemented by

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Properties

Properties

class_

class_: MULTIPLEINPUTFEATUREREQUIREMENT
+

Always 'MultipleInputFeatureRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

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\ No newline at end of file diff --git a/docs/interfaces/NetworkAccessProperties.html b/docs/interfaces/NetworkAccessProperties.html new file mode 100644 index 0000000..94043aa --- /dev/null +++ b/docs/interfaces/NetworkAccessProperties.html @@ -0,0 +1,17 @@ +NetworkAccessProperties | cwl-ts-auto
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Interface NetworkAccessProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#NetworkAccess

+

Indicate whether a process requires outgoing IPv4/IPv6 network +access. Choice of IPv4 or IPv6 is implementation and site +specific, correct tools must support both.

+

If networkAccess is false or not specified, tools must not +assume network access, except for localhost (the loopback device).

+

If networkAccess is true, the tool must be able to make outgoing +connections to network resources. Resources may be on a private +subnet or the public Internet. However, implementations and sites +may apply their own security policies to restrict what is +accessible by the tool.

+

Enabling network access does not imply a publically routable IP +address or the ability to accept inbound connections.

+

Hierarchy

Implemented by

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Properties

Properties

class_

class_: NETWORKACCESS
+

Always 'NetworkAccess'

+

Optional extensionFields

extensionFields?: Dictionary<any>

networkAccess

networkAccess: string | boolean

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\ No newline at end of file diff --git a/docs/interfaces/OperationInputParameterProperties.html b/docs/interfaces/OperationInputParameterProperties.html new file mode 100644 index 0000000..494774d --- /dev/null +++ b/docs/interfaces/OperationInputParameterProperties.html @@ -0,0 +1,86 @@ +OperationInputParameterProperties | cwl-ts-auto
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Interface OperationInputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OperationInputParameter

+

Describe an input parameter of an operation.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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\ No newline at end of file diff --git a/docs/interfaces/OperationOutputParameterProperties.html b/docs/interfaces/OperationOutputParameterProperties.html new file mode 100644 index 0000000..aa225ba --- /dev/null +++ b/docs/interfaces/OperationOutputParameterProperties.html @@ -0,0 +1,61 @@ +OperationOutputParameterProperties | cwl-ts-auto
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Interface OperationOutputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OperationOutputParameter

+

Describe an output parameter of an operation.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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\ No newline at end of file diff --git a/docs/interfaces/OperationProperties.html b/docs/interfaces/OperationProperties.html new file mode 100644 index 0000000..8a135ee --- /dev/null +++ b/docs/interfaces/OperationProperties.html @@ -0,0 +1,57 @@ +OperationProperties | cwl-ts-auto
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Interface OperationProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Operation

+

This record describes an abstract operation. It is a potential +step of a workflow that has not yet been bound to a concrete +implementation. It specifies an input and output signature, but +does not provide enough information to be executed. An +implementation (or other tooling) may provide a means of binding +an Operation to a concrete process (such as Workflow, +CommandLineTool, or ExpressionTool) with a compatible signature.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: OPERATION

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: OperationInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

outputs

outputs: OperationOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

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\ No newline at end of file diff --git a/docs/interfaces/OutputArraySchemaProperties.html b/docs/interfaces/OutputArraySchemaProperties.html new file mode 100644 index 0000000..d917bcb --- /dev/null +++ b/docs/interfaces/OutputArraySchemaProperties.html @@ -0,0 +1,13 @@ +OutputArraySchemaProperties | cwl-ts-auto
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Interface OutputArraySchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputArraySchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Defines the type of the array elements.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: ARRAY
+

Must be array

+

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\ No newline at end of file diff --git a/docs/interfaces/OutputEnumSchemaProperties.html b/docs/interfaces/OutputEnumSchemaProperties.html new file mode 100644 index 0000000..fede219 --- /dev/null +++ b/docs/interfaces/OutputEnumSchemaProperties.html @@ -0,0 +1,13 @@ +OutputEnumSchemaProperties | cwl-ts-auto
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Interface OutputEnumSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputEnumSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

symbols

symbols: string[]
+

Defines the set of valid symbols.

+

type

type: ENUM
+

Must be enum

+

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\ No newline at end of file diff --git a/docs/interfaces/OutputFormatProperties.html b/docs/interfaces/OutputFormatProperties.html new file mode 100644 index 0000000..c24cf6e --- /dev/null +++ b/docs/interfaces/OutputFormatProperties.html @@ -0,0 +1,7 @@ +OutputFormatProperties | cwl-ts-auto
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Interface OutputFormatProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputFormat

+

Hierarchy

Index

Properties

Properties

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

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\ No newline at end of file diff --git a/docs/interfaces/OutputParameterProperties.html b/docs/interfaces/OutputParameterProperties.html new file mode 100644 index 0000000..a294305 --- /dev/null +++ b/docs/interfaces/OutputParameterProperties.html @@ -0,0 +1,58 @@ +OutputParameterProperties | cwl-ts-auto
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Interface OutputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter

+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

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\ No newline at end of file diff --git a/docs/interfaces/OutputRecordFieldProperties.html b/docs/interfaces/OutputRecordFieldProperties.html new file mode 100644 index 0000000..5f2beb4 --- /dev/null +++ b/docs/interfaces/OutputRecordFieldProperties.html @@ -0,0 +1,60 @@ +OutputRecordFieldProperties | cwl-ts-auto
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Interface OutputRecordFieldProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordField

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

name

name: string
+

The name of the field

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

The field type

+

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\ No newline at end of file diff --git a/docs/interfaces/OutputRecordSchemaProperties.html b/docs/interfaces/OutputRecordSchemaProperties.html new file mode 100644 index 0000000..34685b6 --- /dev/null +++ b/docs/interfaces/OutputRecordSchemaProperties.html @@ -0,0 +1,13 @@ +OutputRecordSchemaProperties | cwl-ts-auto
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Interface OutputRecordSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputRecordSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: OutputRecordField[]
+

Defines the fields of the record.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

type

type: RECORD
+

Must be record

+

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Interface OutputSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#OutputSchema

+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional name

name?: string
+

The identifier for this type

+

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Interface ParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Parameter

+

Define an input or output parameter to a process.

+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

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Interface ProcessProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Process

+

The base executable type in CWL is the Process object defined by the +document. Note that the Process object is abstract and cannot be +directly executed.

+

Hierarchy

Index

Properties

Properties

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: (OperationInputParameter | CommandInputParameter | WorkflowInputParameter)[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

outputs

outputs: (CommandOutputParameter | OperationOutputParameter | ExpressionToolOutputParameter | WorkflowOutputParameter)[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

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Interface ProcessRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ProcessRequirement

+

A process requirement declares a prerequisite that may or must be fulfilled +before executing a process. See Process.hints and +Process.requirements.

+

Process requirements are the primary mechanism for specifying extensions to +the CWL core specification.

+

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Interface RecordFieldProperties

+

Auto-generated interface for https://w3id.org/cwl/salad#RecordField

+

A field of a record.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string
+

The name of the field

+

type

type: string | RecordSchema | EnumSchema | ArraySchema | (string | RecordSchema | EnumSchema | ArraySchema)[]
+

The field type

+

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Interface RecordSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: RecordField[]
+

Defines the fields of the record.

+

type

type: RECORD
+

Must be record

+

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Interface ResourceRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ResourceRequirement

+

Specify basic hardware resource requirements.

+

"min" is the minimum amount of a resource that must be reserved to +schedule a job. If "min" cannot be satisfied, the job should not +be run.

+

"max" is the maximum amount of a resource that the job shall be +allocated. If a node has sufficient resources, multiple jobs may +be scheduled on a single node provided each job's "max" resource +requirements are met. If a job attempts to exceed its resource +allocation, an implementation may deny additional resources, which +may result in job failure.

+

If both "min" and "max" are specified, an implementation may +choose to allocate any amount between "min" and "max", with the +actual allocation provided in the runtime object.

+

If "min" is specified but "max" is not, then "max" == "min" +If "max" is specified by "min" is not, then "min" == "max".

+

It is an error if max < min.

+

It is an error if the value of any of these fields is negative.

+

If neither "min" nor "max" is specified for a resource, use the default values below.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: RESOURCEREQUIREMENT
+

Always 'ResourceRequirement'

+

Optional coresMax

coresMax?: string | number
+

Maximum reserved number of CPU cores.

+

See coresMin for discussion about fractional CPU requests.

+

Optional coresMin

coresMin?: string | number
+

Minimum reserved number of CPU cores (default is 1).

+

May be a fractional value to indicate to a scheduling +algorithm that one core can be allocated to multiple +jobs. For example, a value of 0.25 indicates that up to 4 +jobs may run in parallel on 1 core. A value of 1.25 means +that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3).

+

Processes can only share a core allocation if the sum of each +of their ramMax, tmpdirMax, and outdirMax requests also +do not exceed the capacity of the node.

+

Processes sharing a core must have the same level of isolation +(typically a container or VM) that they would normally.

+

The reported number of CPU cores reserved for the process, +which is available to expressions on the CommandLineTool as +runtime.cores, must be a non-zero integer, and may be +calculated by rounding up the cores request to the next whole +number.

+

Scheduling systems may allocate fractional CPU resources by +setting quotas or scheduling weights. Scheduling systems that +do not support fractional CPUs may round up the request to the +next whole number.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional outdirMax

outdirMax?: string | number
+

Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

+

See outdirMin for discussion about fractional storage requests.

+

Optional outdirMin

outdirMin?: string | number
+

Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)

+

May be a fractional value. If so, the actual storage request +must be rounded up to the next whole number. The reported +amount of storage reserved for the process, which is available +to expressions on the CommandLineTool as runtime.outdirSize, +must be a non-zero integer.

+

Optional ramMax

ramMax?: string | number
+

Maximum reserved RAM in mebibytes (2**20)

+

See ramMin for discussion about fractional RAM requests.

+

Optional ramMin

ramMin?: string | number
+

Minimum reserved RAM in mebibytes (2**20) (default is 256)

+

May be a fractional value. If so, the actual RAM request must +be rounded up to the next whole number. The reported amount of +RAM reserved for the process, which is available to +expressions on the CommandLineTool as runtime.ram, must be a +non-zero integer.

+

Optional tmpdirMax

tmpdirMax?: string | number
+

Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

+

See tmpdirMin for discussion about fractional storage requests.

+

Optional tmpdirMin

tmpdirMin?: string | number
+

Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)

+

May be a fractional value. If so, the actual storage request +must be rounded up to the next whole number. The reported +amount of storage reserved for the process, which is available +to expressions on the CommandLineTool as runtime.tmpdirSize, +must be a non-zero integer.

+

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\ No newline at end of file diff --git a/docs/interfaces/ScatterFeatureRequirementProperties.html b/docs/interfaces/ScatterFeatureRequirementProperties.html new file mode 100644 index 0000000..77b4c2d --- /dev/null +++ b/docs/interfaces/ScatterFeatureRequirementProperties.html @@ -0,0 +1,7 @@ +ScatterFeatureRequirementProperties | cwl-ts-auto
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Interface ScatterFeatureRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ScatterFeatureRequirement

+

Indicates that the workflow platform must support the scatter and +scatterMethod fields of WorkflowStep.

+

Hierarchy

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Properties

Properties

class_

class_: SCATTERFEATUREREQUIREMENT
+

Always 'ScatterFeatureRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface SchemaDefRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#SchemaDefRequirement

+

This field consists of an array of type definitions which must be used when +interpreting the inputs and outputs fields. When a type field +contains a IRI, the implementation must check if the type is defined in +schemaDefs and use that definition. If the type is not found in +schemaDefs, it is an error. The entries in schemaDefs must be +processed in the order listed such that later schema definitions may refer +to earlier schema definitions.

+
    +
  • Type definitions are allowed for enum and record types only.
    • +
  • Type definitions may be shared by defining them in a file and then +$include-ing them in the types field.
    • +
  • A file can contain a list of type definitions
    • +
+

Hierarchy

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Index

Properties

Properties

class_

class_: SCHEMADEFREQUIREMENT
+

Always 'SchemaDefRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

types

types: (CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema)[]
+

The list of type definitions.

+

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\ No newline at end of file diff --git a/docs/interfaces/SecondaryFileSchemaProperties.html b/docs/interfaces/SecondaryFileSchemaProperties.html new file mode 100644 index 0000000..772889a --- /dev/null +++ b/docs/interfaces/SecondaryFileSchemaProperties.html @@ -0,0 +1,66 @@ +SecondaryFileSchemaProperties | cwl-ts-auto
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Interface SecondaryFileSchemaProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#SecondaryFileSchema

+

Secondary files are specified using the following micro-DSL for secondary files:

+
    +
  • If the value is a string, it is transformed to an object with two fields +pattern and required
    • +
  • By default, the value of required is null +(this indicates default behavior, which may be based on the context)
    • +
  • If the value ends with a question mark ? the question mark is +stripped off and the value of the field required is set to False
    • +
  • The remaining value is assigned to the field pattern
    • +
+

For implementation details and examples, please see +this section +in the Schema Salad specification.

+

Hierarchy

  • SecondaryFileSchemaProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

pattern

pattern: string
+

Provides a pattern or expression specifying files or directories that +should be included alongside the primary file.

+

If the value is an expression, the value of self in the +expression must be the primary input or output File object to +which this binding applies. The basename, nameroot and +nameext fields must be present in self. For +CommandLineTool inputs the location field must also be +present. For CommandLineTool outputs the path field must +also be present. If secondary files were included on an input +File object as part of the Process invocation, they must also +be present in secondaryFiles on self.

+

The expression must return either: a filename string relative +to the path to the primary File, a File or Directory object +(class: File or class: Directory) with either location +(for inputs) or path (for outputs) and basename fields +set, or an array consisting of strings or File or Directory +objects as previously described.

+

It is legal to use location from a File or Directory object +passed in as input, including location from secondary files +on self. If an expression returns a File object with the +same location but a different basename as a secondary file +that was passed in, the expression result takes precedence. +Setting the basename with an expression this way affects the +path where the secondary file will be staged to in the +CommandLineTool.

+

The expression may return "null" in which case there is no +secondary file from that expression.

+

To work on non-filename-preserving storage systems, portable +tool descriptions should treat location as an opaque +identifier and avoid constructing new values from location, +but should construct relative references using basename or +nameroot instead, or propagate location from defined inputs.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional required

required?: string | boolean
+

An implementation must not fail workflow execution if required is +set to false and the expected secondary file does not exist. +Default value for required field is true for secondary files on +input and false for secondary files on output.

+

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Interface ShellCommandRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ShellCommandRequirement

+

Modify the behavior of CommandLineTool to generate a single string +containing a shell command line. Each item in the argument list must be +joined into a string separated by single spaces and quoted to prevent +intepretation by the shell, unless CommandLineBinding for that argument +contains shellQuote: false. If shellQuote: false is specified, the +argument is joined into the command string without quoting, which allows +the use of shell metacharacters such as | for pipes.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: SHELLCOMMANDREQUIREMENT
+

Always 'ShellCommandRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface SinkProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Sink

+

Hierarchy

Index

Properties

Properties

Optional linkMerge

linkMerge?: LinkMergeMethod
+

The method to use to merge multiple inbound links into a single array. +If not specified, the default method is "merge_nested".

+

Optional pickValue

pickValue?: PickValueMethod
+

The method to use to choose non-null elements among multiple sources.

+

Optional source

source?: string | string[]
+

Specifies one or more workflow parameters that will provide input to +the underlying step parameter.

+

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\ No newline at end of file diff --git a/docs/interfaces/SoftwarePackageProperties.html b/docs/interfaces/SoftwarePackageProperties.html new file mode 100644 index 0000000..1ed2a90 --- /dev/null +++ b/docs/interfaces/SoftwarePackageProperties.html @@ -0,0 +1,47 @@ +SoftwarePackageProperties | cwl-ts-auto
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Interface SoftwarePackageProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#SoftwarePackage

+

Hierarchy

  • SoftwarePackageProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

package_

package_: string
+

The name of the software to be made available. If the name is +common, inconsistent, or otherwise ambiguous it should be combined with +one or more identifiers in the specs field.

+

Optional specs

specs?: string[]
+

One or more IRIs +identifying resources for installing or enabling the software named in +the package field. Implementations may provide resolvers which map +these software identifer IRIs to some configuration action; or they can +use only the name from the package field on a best effort basis.

+

For example, the IRI https://packages.debian.org/bowtie could +be resolved with apt-get install bowtie. The IRI +https://anaconda.org/bioconda/bowtie could be resolved with conda install -c bioconda bowtie.

+

IRIs can also be system independent and used to map to a specific +software installation or selection mechanism. +Using RRID as an example: +https://identifiers.org/rrid/RRID:SCR_005476 +could be fulfilled using the above mentioned Debian or bioconda +package, a local installation managed by Environment Modules, +or any other mechanism the platform chooses. IRIs can also be from +identifer sources that are discipline specific yet still system +independent. As an example, the equivalent ELIXIR Tools and Data +Service Registry IRI to the previous RRID example is +https://bio.tools/tool/bowtie2/version/2.2.8. +If supported by a given registry, implementations are encouraged to +query these system independent sofware identifier IRIs directly for +links to packaging systems.

+

A site specific IRI can be listed as well. For example, an academic +computing cluster using Environment Modules could list the IRI +https://hpc.example.edu/modules/bowtie-tbb/1.22 to indicate that +module load bowtie-tbb/1.1.2 should be executed to make available +bowtie version 1.1.2 compiled with the TBB library prior to running +the accompanying Workflow or CommandLineTool. Note that the example IRI +is specific to a particular institution and computing environment as +the Environment Modules system does not have a common namespace or +standardized naming convention.

+

This last example is the least portable and should only be used if +mechanisms based off of the package field or more generic IRIs are +unavailable or unsuitable. While harmless to other sites, site specific +software IRIs should be left out of shared CWL descriptions to avoid +clutter.

+

Optional version

version?: string[]
+

The (optional) versions of the software that are known to be +compatible.

+

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Interface SoftwareRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#SoftwareRequirement

+

A list of software packages that should be configured in the environment of +the defined process.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: SOFTWAREREQUIREMENT
+

Always 'SoftwareRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

packages

packages: SoftwarePackage[]
+

The list of software to be configured.

+

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Interface StepInputExpressionRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#StepInputExpressionRequirement

+

Indicate that the workflow platform must support the valueFrom field +of WorkflowStepInput.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: STEPINPUTEXPRESSIONREQUIREMENT
+

Always 'StepInputExpressionRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface SubworkflowFeatureRequirementProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement

+

Indicates that the workflow platform must support nested workflows in +the run field of WorkflowStep.

+

Hierarchy

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Properties

Properties

class_

class_: SUBWORKFLOWFEATUREREQUIREMENT
+

Always 'SubworkflowFeatureRequirement'

+

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface ToolTimeLimitProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#ToolTimeLimit

+

Set an upper limit on the execution time of a CommandLineTool. +A CommandLineTool whose execution duration exceeds the time +limit may be preemptively terminated and considered failed. +May also be used by batch systems to make scheduling decisions. +The execution duration excludes external operations, such as +staging of files, pulling a docker image etc, and only counts +wall-time for the execution of the command line itself.

+

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Properties

Properties

class_

class_: TOOLTIMELIMIT
+

Always 'ToolTimeLimit'

+

Optional extensionFields

extensionFields?: Dictionary<any>

timelimit

timelimit: string | number
+

The time limit, in seconds. A time limit of zero means no +time limit. Negative time limits are an error.

+

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Interface WorkReuseProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#WorkReuse

+

For implementations that support reusing output from past work (on +the assumption that same code and same input produce same +results), control whether to enable or disable the reuse behavior +for a particular tool or step (to accomodate situations where that +assumption is incorrect). A reused step is not executed but +instead returns the same output as the original execution.

+

If WorkReuse is not specified, correct tools should assume it +is enabled by default.

+

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Properties

Properties

class_

class_: WORKREUSE
+

Always 'WorkReuse'

+

enableReuse

enableReuse: string | boolean

Optional extensionFields

extensionFields?: Dictionary<any>

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Interface WorkflowInputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowInputParameter

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

The default value to use for this parameter if the parameter is missing +from the input object, or if the value of the parameter in the input +object is null. Default values are applied before evaluating expressions +(e.g. dependent valueFrom fields).

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string | string[]
+

Only valid when type: File or is an array of items: File.

+

This must be one or more IRIs of concept nodes +that represents file formats which are allowed as input to this +parameter, preferrably defined within an ontology. If no ontology is +available, file formats may be tested by exact match.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional inputBinding

inputBinding?: InputBinding
+

Deprecated. Preserved for v1.0 backwards compatability. Will be removed in +CWL v2.0. Use WorkflowInputParameter.loadContents instead.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | InputRecordSchema | InputEnumSchema | InputArraySchema | (string | InputRecordSchema | InputEnumSchema | InputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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Interface WorkflowOutputParameterProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowOutputParameter

+

Describe an output parameter of a workflow. The parameter must be +connected to one or more parameters defined in the workflow that +will provide the value of the output parameter. It is legal to +connect a WorkflowInputParameter to a WorkflowOutputParameter.

+

See WorkflowStepInput for discussion of +linkMerge and pickValue.

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string
+

Only valid when type: File or is an array of items: File.

+

This is the file format that will be assigned to the output +File object.

+

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional linkMerge

linkMerge?: LinkMergeMethod
+

The method to use to merge multiple sources into a single array. +If not specified, the default method is "merge_nested".

+

Optional outputSource

outputSource?: string | string[]
+

Specifies one or more workflow parameters that supply the value of to +the output parameter.

+

Optional pickValue

pickValue?: PickValueMethod
+

The method to use to choose non-null elements among multiple sources.

+

Optional secondaryFiles

secondaryFiles?: SecondaryFileSchema | SecondaryFileSchema[]
+

Only valid when type: File or is an array of items: File.

+

Provides a pattern or expression specifying files or +directories that should be included alongside the primary +file. Secondary files may be required or optional. When not +explicitly specified, secondary files specified for inputs +are required and outputs are optional. An implementation +must include matching Files and Directories in the +secondaryFiles property of the primary file. These Files +and Directories must be transferred and staged alongside the +primary file. An implementation may fail workflow execution +if a required secondary file does not exist.

+

If the value is an expression, the value of self in the expression +must be the primary input or output File object to which this binding +applies. The basename, nameroot and nameext fields must be +present in self. For CommandLineTool outputs the path field must +also be present. The expression must return a filename string relative +to the path to the primary File, a File or Directory object with either +path or location and basename fields set, or an array consisting +of strings or File or Directory objects. It is legal to reference an +unchanged File or Directory object taken from input as a secondaryFile. +The expression may return "null" in which case there is no secondaryFile +from that expression.

+

To work on non-filename-preserving storage systems, portable tool +descriptions should avoid constructing new values from location, but +should construct relative references using basename or nameroot +instead.

+

If a value in secondaryFiles is a string that is not an expression, +it specifies that the following pattern should be applied to the path +of the primary file to yield a filename relative to the primary File:

+
    +
  1. If string ends with ? character, remove the last ? and mark +the resulting secondary file as optional.
    2. +
  2. If string begins with one or more caret ^ characters, for each +caret, remove the last file extension from the path (the last +period . and all following characters). If there are no file +extensions, the path is unchanged.
    3. +
  3. Append the remainder of the string to the end of the file path.
    4. +
+

Optional streamable

streamable?: boolean
+

Only valid when type: File or is an array of items: File.

+

A value of true indicates that the file is read or written +sequentially without seeking. An implementation may use this flag to +indicate whether it is valid to stream file contents using a named +pipe. Default: false.

+

type

type: string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | (string | OutputRecordSchema | OutputEnumSchema | OutputArraySchema)[]
+

Specify valid types of data that may be assigned to this parameter.

+

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Interface WorkflowProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#Workflow

+

A workflow describes a set of steps and the dependencies between +those steps. When a step produces output that will be consumed by a +second step, the first step is a dependency of the second step.

+

When there is a dependency, the workflow engine must execute the preceding +step and wait for it to successfully produce output before executing the +dependent step. If two steps are defined in the workflow graph that +are not directly or indirectly dependent, these steps are independent, +and may execute in any order or execute concurrently. A workflow is +complete when all steps have been executed.

+

Dependencies between parameters are expressed using the source +field on workflow step input parameters and +outputSource field on workflow output +parameters.

+

The source field on each workflow step input parameter expresses +the data links that contribute to the value of the step input +parameter (the "sink"). A workflow step can only begin execution +when every data link connected to a step has been fulfilled.

+

The outputSource field on each workflow step input parameter +expresses the data links that contribute to the value of the +workflow output parameter (the "sink"). Workflow execution cannot +complete successfully until every data link connected to an output +parameter has been fulfilled.

+ + +

Workflow success and failure

+ +

A completed step must result in one of success, temporaryFailure or +permanentFailure states. An implementation may choose to retry a step +execution which resulted in temporaryFailure. An implementation may +choose to either continue running other steps of a workflow, or terminate +immediately upon permanentFailure.

+
    +

  • If any step of a workflow execution results in permanentFailure, then +the workflow status is permanentFailure.

    +
    • +

  • If one or more steps result in temporaryFailure and all other steps +complete success or are not executed, then the workflow status is +temporaryFailure.

    +
    • +

  • If all workflow steps are executed and complete with success, then the +workflow status is success.

    +
    • +
+ + +

Extensions

+ +

ScatterFeatureRequirement and +SubworkflowFeatureRequirement are +available as standard extensions to core +workflow semantics.

+

Hierarchy

Implemented by

Index

Properties

Properties

class_

class_: WORKFLOW

Optional cwlVersion

cwlVersion?: CWLVersion
+

CWL document version. Always required at the document root. Not +required for a Process embedded inside another Process.

+

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this process. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

inputs

inputs: WorkflowInputParameter[]
+

Defines the input parameters of the process. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used to build a user +interface for constructing the input object.

+

When accepting an input object, all input parameters must have a value. +If an input parameter is missing from the input object, it must be +assigned a value of null (or the value of default for that +parameter, if provided) for the purposes of validation and evaluation +of expressions.

+

Optional intent

intent?: string[]
+

An identifier for the type of computational operation, of this Process. +Especially useful for "class: Operation", but can also be used for +CommandLineTool, Workflow, or ExpressionTool.

+

If provided, then this must be an IRI of a concept node that +represents the type of operation, preferrably defined within an ontology.

+

For example, in the domain of bioinformatics, one can use an IRI from +the EDAM Ontology's Operation concept nodes, +like Alignment, +or Clustering; or a more +specific Operation concept like +Split read mapping.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

outputs

outputs: WorkflowOutputParameter[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this process. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

steps

steps: WorkflowStep[]
+

The individual steps that make up the workflow. Each step is executed when all of its +input data links are fufilled. An implementation may choose to execute +the steps in a different order than listed and/or execute steps +concurrently, provided that dependencies between steps are met.

+

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Interface WorkflowStepInputProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepInput

+

The input of a workflow step connects an upstream parameter (from the +workflow inputs, or the outputs of other workflows steps) with the input +parameters of the process specified by the run field. Only input parameters +declared by the target process will be passed through at runtime to the process +though additonal parameters may be specified (for use within valueFrom +expressions for instance) - unconnected or unused parameters do not represent an +error condition.

+ + +

Input object

+ +

A WorkflowStepInput object must contain an id field in the form +#fieldname or #prefix/fieldname. When the id field contains a slash +/ the field name consists of the characters following the final slash +(the prefix portion may contain one or more slashes to indicate scope). +This defines a field of the workflow step input object with the value of +the source parameter(s).

+ + +

Merging multiple inbound data links

+ +

To merge multiple inbound data links, +MultipleInputFeatureRequirement must be specified +in the workflow or workflow step requirements.

+

If the sink parameter is an array, or named in a workflow +scatter operation, there may be multiple inbound +data links listed in the source field. The values from the +input links are merged depending on the method specified in the +linkMerge field. If both linkMerge and pickValue are null +or not specified, and there is more than one element in the +source array, the default method is "merge_nested".

+

If both linkMerge and pickValue are null or not specified, and +there is only a single element in the source, then the input +parameter takes the scalar value from the single input link (it is +not wrapped in a single-list).

+
    +

  • merge_nested

    +

    The input must be an array consisting of exactly one entry for each +input link. If "merge_nested" is specified with a single link, the value +from the link must be wrapped in a single-item list.

    +
    • +

  • merge_flattened

    +
      +
    1. The source and sink parameters must be compatible types, or the source +type must be compatible with single element from the "items" type of +the destination array parameter.
      2. +
    2. Source parameters which are arrays are concatenated. +Source parameters which are single element types are appended as +single elements.
      3. +
    +
    • +
+ + +

Picking non-null values among inbound data links

+ +

If present, pickValue specifies how to picking non-null values among inbound data links.

+

pickValue is evaluated

+
    +
  1. Once all source values from upstream step or parameters are available.
    2. +
  2. After linkMerge.
    3. +
  3. Before scatter or valueFrom.
    4. +
+

This is specifically intended to be useful in combination with +conditional execution, where several upstream +steps may be connected to a single input (source is a list), and +skipped steps produce null values.

+

Static type checkers should check for type consistency after infering what the type +will be after pickValue is applied, just as they do currently for linkMerge.

+
    +

  • first_non_null

    +

    For the first level of a list input, pick the first non-null element. The result is a scalar. +It is an error if there is no non-null element. Examples:

    +
      +
    • [null, x, null, y] -> x
      • +
    • [null, [null], null, y] -> [null]
      • +
    • [null, null, null] -> Runtime Error
      • +
    +

    Intended use case: If-else pattern where the +value comes either from a conditional step or from a default or +fallback value. The conditional step(s) should be placed first in +the list.

    +
    • +

  • the_only_non_null

    +

    For the first level of a list input, pick the single non-null element. The result is a scalar. +It is an error if there is more than one non-null element. Examples:

    +
      +
    • [null, x, null] -> x
      • +
    • [null, x, null, y] -> Runtime Error
      • +
    • [null, [null], null] -> [null]
      • +
    • [null, null, null] -> Runtime Error
      • +
    +

    Intended use case: Switch type patterns where developer considers +more than one active code path as a workflow error +(possibly indicating an error in writing when condition expressions).

    +
    • +

  • all_non_null

    +

    For the first level of a list input, pick all non-null values. +The result is a list, which may be empty. Examples:

    +
      +
    • [null, x, null] -> [x]
      • +
    • [x, null, y] -> [x, y]
      • +
    • [null, [x], [null]] -> [[x], [null]]
      • +
    • [null, null, null] -> []
      • +
    +

    Intended use case: It is valid to have more than one source, but + sources are conditional, so null sources (from skipped steps) + should be filtered out.

    +
    • +
+

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Properties

Properties

Optional default_

default_?: any
+

The default value for this parameter to use if either there is no +source field, or the value produced by the source is null. The +default must be applied prior to scattering or evaluating valueFrom.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

Optional linkMerge

linkMerge?: LinkMergeMethod
+

The method to use to merge multiple inbound links into a single array. +If not specified, the default method is "merge_nested".

+

Optional loadContents

loadContents?: boolean
+

Only valid when type: File or is an array of items: File.

+

If true, the file (or each file in the array) must be a UTF-8 +text file 64 KiB or smaller, and the implementation must read +the entire contents of the file (or file array) and place it +in the contents field of the File object for use by +expressions. If the size of the file is greater than 64 KiB, +the implementation must raise a fatal error.

+

Optional loadListing

loadListing?: LoadListingEnum
+

Only valid when type: Directory or is an array of items: Directory.

+

Specify the desired behavior for loading the listing field of +a Directory object for use by expressions.

+

The order of precedence for loadListing is:

+
    +
  1. loadListing on an individual parameter
    2. +
  2. Inherited from LoadListingRequirement
    3. +
  3. By default: no_listing
    4. +
+

Optional pickValue

pickValue?: PickValueMethod
+

The method to use to choose non-null elements among multiple sources.

+

Optional source

source?: string | string[]
+

Specifies one or more workflow parameters that will provide input to +the underlying step parameter.

+

Optional valueFrom

valueFrom?: string
+

To use valueFrom, StepInputExpressionRequirement must +be specified in the workflow or workflow step requirements.

+

If valueFrom is a constant string value, use this as the value for +this input parameter.

+

If valueFrom is a parameter reference or expression, it must be +evaluated to yield the actual value to be assiged to the input field.

+

The self value in the parameter reference or expression must be

+
    +
  1. null if there is no source field
    2. +
  2. the value of the parameter(s) specified in the source field when this +workflow input parameter is not specified in this workflow step's scatter field.
    3. +
  3. an element of the parameter specified in the source field when this workflow input +parameter is specified in this workflow step's scatter field.
    4. +
+

The value of inputs in the parameter reference or expression must be +the input object to the workflow step after assigning the source +values, applying default, and then scattering. The order of +evaluating valueFrom among step input parameters is undefined and the +result of evaluating valueFrom on a parameter must not be visible to +evaluation of valueFrom on other parameters.

+

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Interface WorkflowStepOutputProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStepOutput

+

Associate an output parameter of the underlying process with a workflow +parameter. The workflow parameter (given in the id field) be may be used +as a source to connect with input parameters of other workflow steps, or +with an output parameter of the process.

+

A unique identifier for this workflow output parameter. This is +the identifier to use in the source field of WorkflowStepInput +to connect the output value to downstream parameters.

+

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Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

The unique identifier for this object.

+

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Interface WorkflowStepProperties

+

Auto-generated interface for https://w3id.org/cwl/cwl#WorkflowStep

+

A workflow step is an executable element of a workflow. It specifies the +underlying process implementation (such as CommandLineTool or another +Workflow) in the run field and connects the input and output parameters +of the underlying process to workflow parameters.

+ + +

Scatter/gather

+ +

To use scatter/gather, +ScatterFeatureRequirement must be specified +in the workflow or workflow step requirements.

+

A "scatter" operation specifies that the associated workflow step or +subworkflow should execute separately over a list of input elements. Each +job making up a scatter operation is independent and may be executed +concurrently.

+

The scatter field specifies one or more input parameters which will be +scattered. An input parameter may be listed more than once. The declared +type of each input parameter is implicitly becomes an array of items of the +input parameter type. If a parameter is listed more than once, it becomes +a nested array. As a result, upstream parameters which are connected to +scattered parameters must be arrays.

+

All output parameter types are also implicitly wrapped in arrays. Each job +in the scatter results in an entry in the output array.

+

If any scattered parameter runtime value is an empty array, all outputs are +set to empty arrays and no work is done for the step, according to +applicable scattering rules.

+

If scatter declares more than one input parameter, scatterMethod +describes how to decompose the input into a discrete set of jobs.

+
    +

  • dotproduct specifies that each of the input arrays are aligned and one + element taken from each array to construct each job. It is an error + if all input arrays are not the same length.

    +
    • +

  • nested_crossproduct specifies the Cartesian product of the inputs, + producing a job for every combination of the scattered inputs. The + output must be nested arrays for each level of scattering, in the + order that the input arrays are listed in the scatter field.

    +
    • +

  • flat_crossproduct specifies the Cartesian product of the inputs, + producing a job for every combination of the scattered inputs. The + output arrays must be flattened to a single level, but otherwise listed in the + order that the input arrays are listed in the scatter field.

    +
    • +
+ + +

Conditional execution (Optional)

+ +

Conditional execution makes execution of a step conditional on an +expression. A step that is not executed is "skipped". A skipped +step produces null for all output parameters.

+

The condition is evaluated after scatter, using the input object +of each individual scatter job. This means over a set of scatter +jobs, some may be executed and some may be skipped. When the +results are gathered, skipped steps must be null in the output +arrays.

+

The when field controls conditional execution. This is an +expression that must be evaluated with inputs bound to the step +input object (or individual scatter job), and returns a boolean +value. It is an error if this expression returns a value other +than true or false.

+

Conditionals in CWL are an optional feature and are not required +to be implemented by all consumers of CWL documents. An +implementation that does not support conditionals must return a +fatal error when attempting execute a workflow that uses +conditional constructs the implementation does not support.

+ + +

Subworkflows

+ +

To specify a nested workflow as part of a workflow step, +SubworkflowFeatureRequirement must be +specified in the workflow or workflow step requirements.

+

It is a fatal error if a workflow directly or indirectly invokes itself as +a subworkflow (recursive workflows are not allowed).

+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

A documentation string for this object, or an array of strings which should be concatenated.

+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hints

hints?: any[]
+

Declares hints applying to either the runtime environment or the +workflow engine that may be helpful in executing this workflow step. It is +not an error if an implementation cannot satisfy all hints, however +the implementation may report a warning.

+

Optional id

id?: string
+

The unique identifier for this object.

+

in_

in_: WorkflowStepInput[]
+

Defines the input parameters of the workflow step. The process is ready to +run when all required input parameters are associated with concrete +values. Input parameters include a schema for each parameter which is +used to validate the input object. It may also be used build a user +interface for constructing the input object.

+

Optional label

label?: string
+

A short, human-readable label of this object.

+

out

out: (string | WorkflowStepOutput)[]
+

Defines the parameters representing the output of the process. May be +used to generate and/or validate the output object.

+

Optional requirements

requirements?: (SoftwareRequirement | InlineJavascriptRequirement | SchemaDefRequirement | LoadListingRequirement | DockerRequirement | InitialWorkDirRequirement | EnvVarRequirement | ShellCommandRequirement | ResourceRequirement | WorkReuse | NetworkAccess | InplaceUpdateRequirement | ToolTimeLimit | SubworkflowFeatureRequirement | ScatterFeatureRequirement | MultipleInputFeatureRequirement | StepInputExpressionRequirement)[]
+

Declares requirements that apply to either the runtime environment or the +workflow engine that must be met in order to execute this workflow step. If +an implementation cannot satisfy all requirements, or a requirement is +listed which is not recognized by the implementation, it is a fatal +error and the implementation must not attempt to run the process, +unless overridden at user option.

+

run

run: string | CommandLineTool | ExpressionTool | Workflow | Operation
+

Specifies the process to run.

+

Optional scatter

scatter?: string | string[]

Optional scatterMethod

scatterMethod?: ScatterMethod
+

Required if scatter is an array of more than one element.

+

Optional when

when?: string
+

If defined, only run the step when the expression evaluates to +true. If false the step is skipped. A skipped step +produces a null on each output.

+

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\ No newline at end of file diff --git a/package.json b/package.json index 423ec15..5a420b1 100644 --- a/package.json +++ b/package.json @@ -1,9 +1,9 @@ { "name": "cwl-ts-auto", - "version": "0.1.0", + "version": "0.1.1", "description": "This project contains TypeScript objects and utilities auto-generated by https://github.com/common-workflow-language/schema_salad for parsing documents corresponding to the https://w3id.org/cwl/cwl# schema.", "author": "Adrian Zimmer", - "homepage" : "https://www.commonwl.org/", + "homepage": "https://www.commonwl.org/", "license": "Apache License, Version 2.0", "repository": { "type": "git", @@ -16,7 +16,8 @@ "types": "dist/index.d.ts", "scripts": { "build": "rm -rf ./dist && tsc", - "test": "nyc --reporter=lcov mocha --require ts-node/register src/test/**/*.ts" + "test": "nyc --reporter=lcov mocha --require ts-node/register src/test/**/*.ts", + "doc": "rm -rf ./docs && typedoc src/index.ts" }, "devDependencies": { "@types/chai": "^4.2.22", @@ -29,12 +30,13 @@ "@types/uuid": "^8.3.3", "chai": "^4.3.4", "chai-as-promised": "^7.1.1", + "codecov.io": "^0.1.6", "mocha": "^9.1.3", "nyc": "^15.1.0", "sinon": "^12.0.1", "ts-node": "^10.4.0", - "typescript": "^4.4.4", - "codecov.io": "^0.1.6" + "typedoc": "^0.22.10", + "typescript": "^4.4.4" }, "dependencies": { "js-yaml": "^4.1.0", @@ -45,4 +47,4 @@ "files": [ "/dist" ] -} \ No newline at end of file +}