Merge branch 'add-sage' into add-test-scripts

Workflomics · Oct 3, 2024 · 9ad38ac · 9ad38ac
2 parents 7081575 + 77e4f60
commit 9ad38ac
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Showing 8 changed files with 28 additions and 4 deletions.
diff --git a/cwl-tools/Sage/sage.cwl → ...tools/Sage-proteomics/Sage-proteomics.cwl b/cwl-tools/Sage/sage.cwl → ...tools/Sage-proteomics/Sage-proteomics.cwl
@@ -32,7 +32,7 @@ inputs:
     default:
       class: File
       format: "http://edamontology.org/format_3464" # JSON
-      location: config.json
+      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/Sage-proteomics/config.json
 
 outputs:
   Sage_out:

diff --git a/cwl-tools/Sage-proteomics/Sage-proteomics.json b/cwl-tools/Sage-proteomics/Sage-proteomics.json
@@ -0,0 +1,24 @@
+{"functions": [{
+    "outputs": [{
+        "format_1915": ["http://edamontology.org/format_3247"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+    }],
+    "biotoolsID": "Sage-proteomics",
+    "inputs": [
+        {
+            "format_1915": ["http://edamontology.org/format_3244"],
+            "data_0006": ["http://edamontology.org/data_0943"]
+        },
+        {
+            "format_1915": ["http://edamontology.org/format_1929"],
+            "data_0006": ["http://edamontology.org/data_2976"]
+        }
+    ],
+    "taxonomyOperations": [
+        "http://edamontology.org/operation_3631",
+        "http://edamontology.org/operation_3633",
+        "http://edamontology.org/operation_2428"
+    ],
+    "label": "Sage",
+    "id": "Sage-proteomics"
+}]}
diff --git a/cwl-tools/Sage/config.json → cwl-tools/Sage-proteomics/config.json b/cwl-tools/Sage/config.json → cwl-tools/Sage-proteomics/config.json
diff --git a/cwl-tools/Sage/sage_TSV_to_mzIdentML.sh → .../Sage-proteomics/sage_TSV_to_mzIdentML.sh b/cwl-tools/Sage/sage_TSV_to_mzIdentML.sh → .../Sage-proteomics/sage_TSV_to_mzIdentML.sh
diff --git a/cwl-tools/Sage/test/debug-in-docker.sh → ...s/Sage-proteomics/test/debug-in-docker.sh b/cwl-tools/Sage/test/debug-in-docker.sh → ...s/Sage-proteomics/test/debug-in-docker.sh
diff --git a/cwl-tools/Sage/test/input.yml → cwl-tools/Sage-proteomics/test/input.yml b/cwl-tools/Sage/test/input.yml → cwl-tools/Sage-proteomics/test/input.yml
diff --git a/cwl-tools/Sage-proteomics/test/run-cwl.sh b/cwl-tools/Sage-proteomics/test/run-cwl.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+cwltool --outdir output ../Sage-proteomics.cwl ./input.yml
diff --git a/cwl-tools/Sage/test/run-cwl.sh b/cwl-tools/Sage/test/run-cwl.sh
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		#!/bin/bash

		cwltool --outdir output ../Sage-proteomics.cwl ./input.yml