define_parset.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.1
class: CommandLineTool
label: define_parset

requirements:
  - class: ShellCommandRequirement
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: input.parset
        entry: |
          steps=[flagedge,flagelev$('is_raw'? ',aoflag,flagamp': '')$(inputs.demix? ',demix': ''),filter,avg]
          #
          flagedge.chan=[0..nchan/32-1,31*nchan/32..nchan-1]
          flagedge.type=preflagger
          #
          aoflag.keepstatistics=true
          aoflag.memoryperc=20
          aoflag.type=aoflagger
          aoflag.autocorr=$(inputs.flag_autocorrelation?'True':'False')
          aoflag.strategy=/usr/local/share/aoflagger/strategies/lofar-default.lua
          #
          flagelev.type=preflagger
          flagelev.elevation=0deg..20deg
          #
          flagamp.amplmin=1e-30
          flagamp.type=preflagger
          #
          filter.baseline="[CR]S*&"
          filter.remove=True
          filter.type=filter
          #
          avg.type=average
          avg.timeresolution=4.0
          avg.freqresolution=48828.125Hz


inputs:
- id: flag_autocorrelation
  type: boolean?
  default: true
- id: is_raw
  type: boolean
  default: true

outputs:
- id: output
  type: File
  outputBinding:
    glob: preproc.parset

baseCommand:
- cp
arguments:
- prefix: ''
  position: 0
  valueFrom: input.parset
  shellQuote: false
- prefix: ''
  position: 0
  valueFrom: preproc.parset
  shellQuote: false
id: define_parset