Merge branch 'losoto_duplicate' into 'master'

Add LoSoTo Duplicate step

See merge request eosc/prefactor3-cwl!15

Former-commit-id: 20a52b73

.gitlab-ci.yml

@@ -68,6 +68,12 @@ losoto_abs:
   script:
     - cwl-runner --no-container steps/LoSoTo.Abs.cwl test_jobs/losoto_abs.json
 
+losoto_duplicate:
+  stage: test_steps
+  allow_failure: true
+  scripts:
+    - cwl-runner --no-container steps/LoSoTo.Duplicate.cwl test_jobs/losoto_duplicate.json
+
 losoto_plot:
   stage: test_steps
   allow_failure: true

steps/LoSoTo.Duplicate.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_duplicate
+
+doc: |
+  Duplicate a table
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'parset.config'
+        entry: |
+          [duplicate]
+          soltab = $(inputs.soltab)
+          operation = DUPLICATE
+          $(inputs.soltabOut !== null? 'soltabOut=' + inputs.soltabOut: '')
+
+      - entryname: $(inputs.input_h5parm.basename)
+        entry: $(inputs.input_h5parm)
+        writable: true
+
+baseCommand: "losoto"
+
+arguments:
+  - $(inputs.input_h5parm.basename)
+  - parset.config
+
+hints:
+  DockerRequirement:
+    dockerPull: lofareosc/prefactor-ci:master
+
+inputs:
+  - id: input_h5parm
+    type: File
+  - id: soltab
+    type: string
+    doc: "Solution table"
+  - id: soltabOut 
+    type: string?
+    doc: Output table name. By default choose next available from table type.
+outputs:
+  - id: output_h5parm
+    type: File
+    outputBinding:
+      glob: $(inputs.input_h5parm.basename)

test_jobs/losoto_duplicate.cwl

+{
+    "input_h5parm": {
+            "class": "File",
+            "path": "/data/example.h5"
+        },
+    "soltab": "sol000/amplitude000"
+}