Merge branch 'LoSoTo-Faraday' into 'master'

Add LoSoTo Faraday - Resolve EOSC-24

See merge request !4

.gitlab-ci.yml

@@ -111,6 +111,12 @@ losoto_clip:
   script:
     - cwl-runner --no-container steps/LoSoTo.Clip.cwl test_jobs/losoto_clip.json
 
+losoto_faraday:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwl-runner --no-container steps/LoSoTo.Faraday.cwl test_jobs/losoto_faraday.json
+
 losoto_residual:
   stage: test_steps
   allow_failure: true

steps/LoSoTo.Faraday.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_faraday
+
+$namespaces:
+  lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+  Faraday rotation extraction from either a rotation table or a
+  circular phase (of which the operation get the polarisation difference).
+
+
+requirements:
+  InlineJavascriptRequirement:
+    expressionLib:
+      - { $include: utils.js}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'parset.config'
+        entry: $(get_losoto_config('FARADAY').join('\n'))
+
+      - entryname: $(inputs.input_h5parm.basename)
+        entry: $(inputs.input_h5parm)
+        writable: true
+
+baseCommand: "losoto"
+
+arguments:
+  - $(inputs.input_h5parm.basename)
+  - parset.config
+
+hints:
+  DockerRequirement:
+    dockerPull: lofareosc/lofar-pipeline-ci:latest
+
+inputs:
+  - id: input_h5parm
+    type: File
+    format: lofar:#H5Parm
+  - id: soltab
+    type: string
+    doc: "Solution table"
+  - id: refAnt
+    type: string?
+    doc:  Reference antenna, by default the first.
+  - id: maxResidual
+    type: float?
+    doc: |
+      Max average residual in radians before flagging datapoint,
+      by default 1. If 0: no check.
+
+
+outputs:
+  - id: output_h5parm
+    type: File
+    format: lofar:#H5Parm
+    outputBinding:
+      glob: $(inputs.input_h5parm.basename)
+$schema:
+  - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl

test_jobs/losoto_faraday.json

+{
+  "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+  "soltab":  "sol000/phase000",
+  "ncpu": 1
+}