preprocess.cwl

cwlVersion: v1.2
class: CommandLineTool
baseCommand: DP3
label: Performs pre-processing on raw LOFAR data.
doc: |
  This tool performs flagging, demixing, averaging, and Dysco compression on 
  raw LOFAR data with the Default Pre-Processing Pipeline (DP3). The input is 
  a raw LOFAR MeasurementSet (MS); to open raw MSs, the LOFAR Storage Manager 
  (LofarStMan) needs to be installed. The output is a pre-processed MS, which 
  can further be processed by, e.g., the LOFAR Initial Calibration (LINC) Pipeline.

arguments:
  - steps=[aoflagger,demix]
  - msin.autoweight=true
  - msout.storagemanager=dysco

inputs:
  - id: msin
    type: Directory
    inputBinding:
      prefix: msin=
      separate: false
    doc: Input raw LOFAR MS
  - id: rfistrategy
    type:
      - string?
      - File?
    inputBinding:
      prefix: aoflagger.strategy=
      separate: false
    default:
      class: File
      path: ../rfistrategies/lofar-default.lua
    doc: AOFlagger flagging strategy file
  - id: demix_skymodel
    type:
      - string?
      - File?
    inputBinding:
      prefix: demix.skymodel=
      separate: false
    default:
      class: File
      path: ../skymodels/Ateam.skymodel
    doc: Skymodel to use for calibration
  - id: demix_sources
    type: string[]?
    inputBinding:
      prefix: demix.subtractsoures=
      separate: false
    default: []
    doc: Sources to subtract during demixing
  - id: demix_timestep
    type: int
    inputBinding:
      prefix: demix.demixtimestep=
      separate: false
    doc: Number of time steps to average during demixing
  - id: demix_freqstep
    type: int
    inputBinding:
      prefix: demix.demixfreqstep=
      separate: false
    doc: Number of channels to average during demixing
  - id: avg_timestep
    type: int
    inputBinding:
      prefix: demix.timestep=
      separate: false
    doc: Number of time steps to average
  - id: avg_freqstep
    type: int
    inputBinding:
      prefix: demix.freqstep=
      separate: false
    doc: Number of channels to average
  - id: msout_name
    type: string
    inputBinding:
      prefix: msout=
      separate: false
    doc: Output MS

outputs:
  - id: msout
    type: Directory
    outputBinding:
      glob: '$(inputs.msout_name == "." ? inputs.msin.basename : inputs.msout_name)'
    doc: Output MS

requirements:
  InlineJavascriptRequirement: {}