Update Galaxy Tools (#65)

qiime2 · Apr 25, 2024 · 389df01 · 389df01
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diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>De novo multiple sequence alignment with MAFFT</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be aligned.">
@@ -28,18 +28,6 @@ for:
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <conditional name="__q2galaxy__GUI__conditional__n_threads__">
-                <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores)">
-                    <option value="auto">auto (Str)</option>
-                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
-                </param>
-                <when value="auto">
-                    <param name="n_threads" type="hidden" value="auto"/>
-                </when>
-                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
-                    <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores)"/>
-                </when>
-            </conditional>
             <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No]  This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
         </section>
     </inputs>

diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Add sequences to multiple sequence alignment with MAFFT.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to which sequences should be added.">
@@ -34,18 +34,6 @@ for:
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <conditional name="__q2galaxy__GUI__conditional__n_threads__">
-                <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores)">
-                    <option value="auto">auto (Str)</option>
-                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
-                </param>
-                <when value="auto">
-                    <param name="n_threads" type="hidden" value="auto"/>
-                </when>
-                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
-                    <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores)"/>
-                </when>
-            </conditional>
             <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No]  This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
             <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No]  Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
         </section>

diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Positional conservation and gap filtering.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mask '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to be masked.">

diff --git a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Add pseudocount to table.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition add_pseudocount '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to which pseudocounts should be added.">

diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 composition ancom" id="qiime2__composition__ancom" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition ancom" id="qiime2__composition__ancom" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Apply ANCOM to identify features that differ in abundance.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition ancom '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Composition]" help="[required]  The feature table to be used for ANCOM computation.">

diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Analysis of Composition of Microbiomes with Bias Correction</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition ancombc '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to be used for ANCOM-BC computation.">
@@ -68,7 +68,6 @@ for:
                     <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
                 </param>
             </repeat>
-            <param name="neg_lb" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="neg_lb: Bool" help="[default: No]  Whether to classify a taxon as a structural zero using its asymptotic lower bound."/>
             <param name="tol" type="float" value="1e-05" label="tol: Float" help="[default: 1e-05]  The iteration convergence tolerance for the E-M algorithm."/>
             <param name="max_iter" type="integer" value="100" label="max_iter: Int" help="[default: 100]  The maximum number of iterations for the E-M algorithm."/>
             <param name="conserve" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="conserve: Bool" help="[default: No]  Whether to use a conservative variance estimator for the test statistic. It is recommended if the sample size is small and/or the number of differentially abundant taxa is believed to be large."/>

diff --git a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Differential abundance bar plots</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition da_barplot '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required]  The ANCOM-BC output to be plotted.">
@@ -80,6 +80,7 @@ for:
                     </param>
                 </when>
             </conditional>
+            <param name="label_limit" type="integer" optional="true" label="label_limit: Int" help="[optional]  Set the maximum length that will be viewable for axis labels. You can set this parameter if your axis labels are being cut off."/>
         </section>
     </inputs>
     <outputs>

diff --git a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description> View tabular output from ANCOM-BC.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required]  The ANCOM-BC output to be tabulated.">

diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza
diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza