Draft: Add facetselfcal to VLBI-pipeline

Adding facetselfcal to the VLBI-pipeline as a single CWL step

steps/facet_selfcal.cwl

+class: CommandLineTool
+cwlVersion: v1.2
+id: facet_selfcal
+label: facet_selfcal
+inputs:
+  - id: facetselfcal
+    type: File
+    doc: facet_selfcal script to be exectued
+  - id: msin
+    type: Directory[]
+    doc: Input measurement sets
+    inputBinding:
+      position: 1
+  - id: boxfile
+    type: File?
+    inputBinding:
+      position: 0
+      prefix: --boxfile=
+      separate: false
+      shellQuote: false
+  - id: imsize
+    type: int?
+    default: 1600
+    inputBinding:
+      position: 0
+      prefix: --imsize=
+      separate: false
+      shellQuote: false
+  - id: pixelscale
+    type: float?
+    default: 0.075
+    inputBinding:
+      position: 0
+      prefix: --pixelscale=
+      separate: false
+      shellQuote: false
+  - id: imagename
+    type: string?
+    inputBinding:
+      position: 0
+      prefix: --imagename=
+      separate: false
+      shellQuote: false
+  - id: fitsmask
+    type: File?
+    inputBinding:
+      position: 0
+      prefix: --fitsmask=
+      separate: false
+      shellQuote: false
+  - id: niter
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --niter=
+      separate: false
+      shellQuote: false
+  - id: robust
+    type: float?
+    default: -0.5
+    inputBinding:
+      position: 0
+      prefix: --robust=
+      separate: false
+      shellQuote: false
+  - id: channelsout
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --channelsout=
+      separate: false
+      shellQuote: false
+  - id: multiscale
+    type: boolean?
+    default: false
+    inputBinding:
+      position: 0
+      prefix: --multiscale
+  - id: multiscale-start
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --multiscale-start=
+      separate: false
+      shellQuote: false
+  - id: multiscalescalebias
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --multiscalescalebias=
+      separate: false
+      shellQuote: false
+  - id: deepmultiscale
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --deepmultiscale
+  - id: uvminim
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --uvminim=
+      separate: false
+      shellQuote: false
+  - id: usewgridder
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --usewgridder=True
+  - id: phaseupstations
+    type: string?
+    default: 'core'
+    inputBinding:
+      position: 0
+      prefix: --phaseupstations=
+      separate: false
+      shellQuote: false
+  - id: phaseshiftbox
+    type: File?
+    inputBinding:
+      position: 0
+      prefix: --phaseshiftbox=
+  - id: paralleldeconvolution
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --paralleldeconvolution=
+      separate: false
+      shellQuote: false
+  - id: parallelgridding
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --parallelgridding=
+      separate: false
+      shellQuote: false
+  - id: deconvolutionchannels
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --deconvolutionchannels=
+      separate: false
+      shellQuote: false
+  - id: idg
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --idg
+  - id: maskthreshold
+    type: float[]?
+    default:
+      - 7.0
+    inputBinding:
+      position: 0
+      prefix: --maskthreshold=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: imager
+    type: string?
+    inputBinding:
+      position: 0
+      prefix: --imager=
+      separate: false
+      shellQuote: false
+  - id: fitspectralpol
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --fitspectralpol=True
+      separate: false
+      shellQuote: false
+  - id: fitspectralpolorder
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --fitspectralpolorder
+      separate: false
+      shellQuote: false
+  - id: taperinnertukey
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --taperinnertukey=
+      separate: false
+      shellQuote: false
+  - id: removenegativefrommodel
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --removenegativefrommodel=True
+  - id: autoupdate-removenegativefrommodel
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --autoupdate-removenegativefrommodel=True
+  - id: autofrequencyaverage
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --autofrequencyaverage
+  - id: autofrequencyaverage-calspeedup
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --autofrequencyaverage-calspeedup
+  - id: avgfreqstep
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --avgfreqstep=
+      separate: false
+      shellQuote: false
+  - id: avgtimestep
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --avgtimestep=
+      separate: false
+      shellQuote: false
+  - id: msinnchan
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --msinnchan=
+      separate: false
+      shellQuote: false
+  - id: msinntimes
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --msinntimes=
+      separate: false
+      shellQuote: false
+  - id: weightspectrum-clipvalue
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --weightspectrum-clipvalue=
+      separate: false
+      shellQuote: false
+  - id: --uvmin
+    type: float?
+    default: 40000.0
+    inputBinding:
+      position: 0
+      prefix: --uvmin=
+      separate: false
+      shellQuote: false
+  - id: uvminscalarphasediff
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --uvminscalarphasediff=
+      separate: false
+      shellQuote: false
+  - id: update-uvmin
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --update-uvmin=
+  - id: update-multiscale
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --update-multiscale=
+  - id: soltype-list
+    type: string[]?
+    default:
+      - "\"scalarphasediff\""
+      - "\"scalarphase\""
+      - "\"scalarcomplexgain\""
+    inputBinding:
+      position: 0
+      prefix: --soltype-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: solint-list
+    type: int[]?
+    default:
+      - 4
+      - 1
+      - 100
+    inputBinding:
+      position: 0
+      prefix: --solint-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: nchan-list
+    type: int[]?
+    default:
+      - 1
+      - 1
+      - 1
+    inputBinding:
+      position: 0
+      prefix: --nchan-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: smoothnessconstraint-list
+    type: float[]?
+    default:
+      - 10.0
+      - 2.0
+      - 10.0
+    inputBinding:
+      position: 0
+      prefix: --smoothnessconstraint-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: smoothnessreffrequency-list
+    type: float[]?
+    inputBinding:
+      position: 0
+      prefix: --smoothnessreffrequency-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: smoothnessspectralexponent-list
+    type: float[]?
+    inputBinding:
+      position: 0
+      prefix: --smoothnessspectralexponent-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: smoothnessrefdistance-list
+    type: float[]?
+    inputBinding:
+      position: 0
+      prefix: --smoothnessrefdistance-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: antennaconstraint-list
+    type: string[]?
+    default:
+      - "\"alldutch\""
+      - None
+      - None
+    inputBinding:
+      position: 0
+      prefix: --antennaconstraint-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: resetsols-list
+    type: float[]?
+    inputBinding:
+      position: 0
+      prefix: --resetsols-list=
+      separate: false
+      shellQuote: false
+  - id: soltypecycles-list
+    type: int[]?
+    default:
+      - 0
+      - 0
+      - 2
+    inputBinding:
+      position: 0
+      prefix: --soltypecycles-list=
+      separate: false
+      shellQuote: false
+      valueFrom: "[$(self.join(','))]"
+  - id: BLsmooth
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --BLsmooth
+  - id: iontimefactor
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --iontimefactor=
+      separate: false
+      shellQuote: false
+  - id: ionfreqfactor
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --ionfreqfactor=
+      separate: false
+      shellQuote: false
+  - id: blscalefactor
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --blscalefactor=
+      separate: false
+      shellQuote: false
+  - id: dejumpFR
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --dejumpFR
+  - id: usemodeldataforsolints
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --usemodeldataforsolints=
+  - id: tecfactorsolint
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --tecfactorsolint=
+      separate: false
+      shellQuote: false
+  - id: gainfactorsolint
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --gainfactorsolint=
+      separate: false
+      shellQuote: false
+  - id: phasefactorsolint
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --phasefactorsolint=
+      separate: false
+      shellQuote: false
+  - id: preapplyH5-list
+    type: File[]?
+    inputBinding:
+      position: 0
+      prefix: --preapplyH5-list=
+      separate: false
+      shellQuote: false
+  - id: skymodel
+    type: File?
+    inputBinding:
+      position: 0
+      prefix: --skymodel=
+      separate: false
+      shellQuote: false
+  - id: skymodelsource
+    type: string?
+    inputBinding:
+      position: 0
+      prefix: --skymodelsource=
+      separate: false
+      shellQuote: false
+  - id: skymodelpointsource
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --skymodelpointsource=
+      separate: false
+      shellQuote: false
+  - id: wscleanskymodel
+    type: File?
+    inputBinding:
+      position: 0
+      prefix: --wscleanskymodel=
+      separate: false
+      shellQuote: false
+  - id: predictskywithbeam
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --predictskywithbeam
+  - id: startfromtgss
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --startfromtgss
+  - id: startfromvlass
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --startfromvlass
+  - id: tgssfitsimage
+    type: File?
+    inputBinding:
+      position: 0
+      prefix: --tgssfitsimage=
+      separate: false
+      shellQuote: false
+  - id: no-beamcor
+    type: boolean?
+    default: True
+    inputBinding:
+      position: 0
+      prefix: --no-beamcor
+  - id: losotobeamcor-beamlib
+    type: string?
+    inputBinding:
+      position: 0
+      prefix: --losotobeamcor-beamlib=
+      separate: false
+      shellQuote: false
+  - id: docircular
+    type: boolean?
+    default: True
+    inputBinding:
+      position: 0
+      prefix: --docircular
+  - id: dolinear
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --dolinear
+  - id: forwidefield
+    default: True
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --forwidefield
+  - id: doflagging
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --doflagging=True
+  - id: dysco
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --dysco=True
+      separate: false
+      shellQuote: false
+  - id: restoreflags
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --restoreflags
+  - id: remove-flagged-from-startend
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --remove-flagged-from-startend
+  - id: flagslowamprms
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --flagslowamprms=
+      separate: false
+      shellQuote: false
+  - id: flagslowphaserms
+    type: float?
+    inputBinding:
+      position: 0
+      prefix: --flagslowphaserms=
+      separate: false
+      shellQuote: false
+  - id: doflagslowphases
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --doflagslowphases=True
+  - id: useaoflagger
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --useaoflagger
+  - id: useaoflaggerbeforeavg
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --useaoflaggerbeforeavg=True
+  - id: normamps
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --normamps=True
+  - id: normampsskymodel
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --normampsskymodel=True
+  - id: resetweights
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --resetweights
+  - id: start
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --start=
+      separate: false
+      shellQuote: false
+  - id: stop
+    type: int?
+    default: 10
+    inputBinding:
+      position: 0
+      prefix: --stop=
+      separate: false
+      shellQuote: false
+  - id: stopafterskysolve
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --stopafterskysolve
+  - id: noarchive
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --noarchive
+  - id: skipbackup
+    type: boolean?
+    default: True
+    inputBinding:
+      position: 0
+      prefix: --skipbackup
+  - id: helperscriptspath
+    type: Directory
+    inputBinding:
+      position: 0
+      prefix: --helperscriptspath=
+      separate: false
+      shellQuote: false
+  - id: helperscriptspathh5merge
+    type: Directory
+    inputBinding:
+      position: 0
+      prefix: --helperscriptspathh5merge=
+      separate: false
+      shellQuote: false
+  - id: auto
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --auto
+  - id: delaycal
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --delaycal
+  - id: targetcalILT
+    type: string?
+    inputBinding:
+      position: 0
+      prefix: --targetcalILT=
+      separate: false
+      shellQuote: false
+  - id: makeimage-ILTlowres-HBA
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --makeimage-ILTlowres-HBA
+  - id: makeimage-fullpol
+    type: boolean?
+    inputBinding:
+      position: 0
+      prefix: --makeimage-fullpol
+  - id: blsmooth_chunking_size
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: --blsmooth_chunking_size=
+      separate: false
+      shellQuote: false
+outputs:
+  - id: output_plots
+    type: Directory[]
+    outputBinding:
+      glob: 'plotlosoto*'
+  - id: solutions
+    type: File[]
+    outputBinding:
+      glob: '*.h5'
+  - id: fits_images
+    type: File[]
+    outputBinding:
+      glob: '*.fits'
+  - id: png_images
+    type: File[]
+    outputBinding:
+      glob: '*.png'
+  - id: logfile
+    type: File
+    outputBinding:
+      glob: 'selfcal.log'
+baseCommand: python3
+arguments:
+  - $(inputs.facetselfcal)
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+      - entry: $(inputs.helperscriptspath)
+        writable: false
+  - class: InlineJavascriptRequirement
+stdout: facet_selfcal.log
+stderr: facet_selfcal_err.log
\ No newline at end of file