Some workflow test updates

topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow-test.yml

@@ -0,0 +1,30 @@
+---
+- doc: Test Analysis of molecular dynamics simulations workflow
+  job:
+    protein_pdb:
+      class: File
+      location: https://zenodo.org/record/2537734/files/cbh1test.pdb
+      filetype: pdb
+    protein_mdsimulation_dcd:
+      class: File
+      location: https://zenodo.org/record/2537734/files/cbh1test.dcd
+      filetype: dcd
+  outputs:
+    rmsf_tabular_output:
+      asserts:
+        has_n_columns:
+          n: 2
+        has_line_matching:
+          expression: 1\s+0.29.*
+    pca_tabular_output:
+      asserts:
+        has_n_columns:
+          n: 4
+        has_line_matching:
+          expression: 1\s+0.047.*\s+0.0374.*\s+0.0436.*
+    rmsd_tabular_output:
+      asserts:
+        has_n_columns:
+          n: 2
+        has_line_matching:
+          expression: 2\s+0.21*

topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga

@@ -13,18 +13,18 @@
       "inputs": [
         {
           "description": "",
-          "name": "dcd_trajectory_output_40.dcd_2.dcd"
+          "name": "protein_mdsimulation_dcd"
         }
       ],
-      "label": "dcd_trajectory_output_40.dcd_2.dcd",
+      "label": "protein_mdsimulation_dcd",
       "name": "Input dataset",
       "outputs": [],
       "position": {
         "left": 200,
         "top": 310
       },
       "tool_id": null,
-      "tool_state": "{\"name\": \"dcd_trajectory_output_40.dcd_2.dcd\"}",
+      "tool_state": "{\"name\": \"protein_mdsimulation_dcd\"}",
       "tool_version": null,
       "type": "data_input",
       "uuid": "e26cd82e-19c8-4cf5-93c7-5a0a0e5201cc",
@@ -39,18 +39,18 @@
       "inputs": [
         {
           "description": "",
-          "name": "minimizer_pdb_8.pdb_1.pdb"
+          "name": "protein_pdb"
         }
       ],
-      "label": "minimizer_pdb_8.pdb_1.pdb",
+      "label": "protein_pdb",
       "name": "Input dataset",
       "outputs": [],
       "position": {
         "left": 200,
         "top": 430
       },
       "tool_id": null,
-      "tool_state": "{\"name\": \"minimizer_pdb_8.pdb_1.pdb\"}",
+      "tool_state": "{\"name\": \"protein_pdb\"}",
       "tool_version": null,
       "type": "data_input",
       "uuid": "cbe0e7c8-c572-4231-a55f-d04c72760cd4",
@@ -113,7 +113,13 @@
       "tool_version": "2.3",
       "type": "tool",
       "uuid": "5b0988f7-6cb1-4dfc-95b5-d5493d77d579",
-      "workflow_outputs": []
+      "workflow_outputs": [
+        {
+          "label": "rmsd_tabular_output",
+          "output_name": "output",
+          "uuid": "6de2beaf-f80e-4788-8598-229a1c582757"
+        }
+      ]
     },
     "3": {
       "annotation": "",
@@ -168,7 +174,13 @@
       "tool_version": "2.3",
       "type": "tool",
       "uuid": "aebc72d2-95bd-4b94-aa49-f8fbd55e7d54",
-      "workflow_outputs": []
+      "workflow_outputs": [
+        {
+          "label": "rmsf_tabular_output",
+          "output_name": "output",
+          "uuid": "1f2d715d-230a-4ec5-a509-e8ae501e7634"
+        }
+      ]
     },
     "4": {
       "annotation": "",
@@ -231,7 +243,13 @@
       "tool_version": "2.3",
       "type": "tool",
       "uuid": "99415486-79b9-47d1-8111-02d0e6dcbed6",
-      "workflow_outputs": []
+      "workflow_outputs": [
+        {
+          "label": "pca_tabular_output",
+          "output_name": "output",
+          "uuid": "92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5"
+        }
+      ]
     }
   },
   "tags": [

topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md

@@ -89,7 +89,7 @@ A prepared file is available via Zenodo. Alternatively, you can prepare the file
 > ### {% icon comment %} Alternative upload
 > As an alternative option, if you prefer to upload the cleaned file directly from Zenodo, you can do so with the following link:
 >    ```
->    https://zenodo.org/record/2598415
+>    https://zenodo.org/record/2598415/files/1AKI_clean.pdb
 >    ```
 >    {% include snippets/import_via_link.md %}
 {: .comment}

topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow-test.yml

@@ -0,0 +1,14 @@
+---
+- doc: Test GROMACS Training workflow
+  job: {}
+  outputs:
+    gro_output:
+      asserts:
+        has_text:
+          text: "LYSOZYME in water"
+    xtc_output:
+      asserts:
+        has_size: 
+          value: 2337500
+          delta: 30000
+

topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow.ga

@@ -636,8 +636,17 @@
                "name":"report"
             }
          ],
-         "workflow_outputs":[
-
+         "workflow_outputs": [
+            {
+               "label": "xtc_output",
+               "output_name": "output4",
+               "uuid": "027305f5-213b-40af-8e2b-c376d5d2e294"
+            },
+            {
+               "label": "gro_output",
+               "output_name": "output1",
+               "uuid": "e745fd4c-f607-4215-84e4-c62587c8c07a"
+            }
          ],
          "input_connections":{
             "top_input":{

topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-job.yml

@@ -1,19 +1,19 @@
 ---
-silva:
+'SILVA Reference':
   class: File
   location: https://zenodo.org/record/815875/files/silva.v4.fasta
   filetype: fasta
-anguil_soil_sample:
+'Anguil Soil Sample':
   class: File
   location: https://zenodo.org/record/815875/files/SRR651839_anguil.fasta
   filetype: fasta
-pampa_soil_sample:
+'Pampa Soil Sample':
   class: File
   location: https://zenodo.org/record/815875/files/SRR531818_pampa.fasta
-trainset_alignment:
+'Trainset PDS alignment':
   class: File
   location: https://zenodo.org/record/815875/files/trainset16_022016.pds.fasta
-trainset_taxonomy:
+'Trainset PDS taxonomy':
   class: File
   location: https://zenodo.org/record/815875/files/trainset16_022016.pds.tax
   filetype: mothur.seq.taxonomy

topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-test.yml

@@ -5,4 +5,4 @@
     mothur_make_shared_shared:
       asserts:
         has_text:
-          text: "0.03	anguil	4015	250	145	167	181	122"
+          text: "0.03	anguil"

topics/proteomics/tutorials/protein-quant-sil/workflows/workflow-test.yml

@@ -0,0 +1,17 @@
+---
+- doc: Test ID Plus Quant SIL Training workflow
+  job:
+    'mzML file':
+      class: File
+      location: https://zenodo.org/record/1051552/files/HEK_SILAC-K6R6_ST905_part.mzml
+      filetype: mzml
+    'fasta file':
+      class: File
+      location: https://zenodo.org/record/892005/files/Human_database_including_decoys_%28cRAP_added%29.fasta
+      filetype: fasta
+  outputs:
+    protein_quant:
+      asserts:
+        has_text_matching:
+          expression: '"sp|P61604|CH10_HUMAN"\s+1\s+0.99'
+

topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga

@@ -861,7 +861,7 @@
         {
           "output_name": "param_out",
           "uuid": "c5ec6e2a-8a27-447a-a3ad-28a79954143b",
-          "label": null
+          "label": "protein_quant"
         }
       ],
       "input_connections": {