summary.cwl

class: CommandLineTool
cwlVersion: v1.1
$namespaces:
  lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
  sbg: 'https://www.sevenbridges.com/'
id: summary
baseCommand:
  - make_summary_CWL.py
inputs:
  - id: flagFiles
    type:
      - 'File[]'
      - File
    inputBinding:
      position: 1
    doc: List of files with flag information (JSON)
  - id: pipeline
    type: string?
    default: 'prefactor'
    inputBinding:
      position: 0
      prefix: '--pipeline'
    doc: Name of the pipeline
  - id: run_type
    default: 'calibrator'
    type: string?
    inputBinding:
      position: 0
      prefix: '--run_type'
    doc: Type of the pipeline
  - id: filter
    default: '*&'
    type: string?
    inputBinding:
      position: 0
      prefix: '--filtered_antennas'
    doc: Filter these antenna string from the processing.
  - id: bad_antennas
    default: '*&'
    type: string?
    inputBinding:
      position: 0
      prefix: '--bad_antennas'
    doc: Antenna string to be processed
  - id: structure_file
    default: false
    type: 
      - boolean?
      - File?
    inputBinding:
      position: 0
      prefix: '--structure_file'
  - id: Ateam_separation_file
    default: false
    type: 
      - boolean?
      - File?
    inputBinding:
      position: 0
      prefix: '--Ateam_separation_file'
  - id: solutions
    default: false
    type: 
      - boolean?
      - File?
    inputBinding:
      position: 0
      prefix: '--solutions'
  - id: clip_sources
    default: false
    type: 
      - string?
      - boolean?
    inputBinding:
      position: 0
      prefix: '--clip_sources'
      separate: true
      itemSeparator: ','
      valueFrom: '$(self)'
  - id: demix_sources
    default: false
    type:
      - string?
      - boolean?
    inputBinding:
      position: 0
      prefix: '--demix_sources'
      separate: true
      itemSeparator: ','
      valueFrom: '$(self)'
  - id: removed_bands
    default: false
    type:
      - string?
      - boolean?
    inputBinding:
      position: 0
      prefix: '--removed_bands'
      separate: true
      itemSeparator: ','
      valueFrom: '$(self)'
  - id: min_unflagged_fraction
    default: 0.5
    type: float?
    inputBinding:
      position: 0
      prefix: '--min_unflagged'
    doc: minimum fraction of unflagged data per band to continue
  - id: demix
    default: false
    type: boolean?
    inputBinding:
      position: 0
      prefix: '--demix True'
  - id: refant
    default: ''
    type: string?
    inputBinding:
      position: 0
      prefix: '--refant'
    doc: Reference antenna used
  - id: output_fname
    type: 
      - boolean?
      - string?
    default: false
    inputBinding:
      position: 0
      prefix: '--output_fname'
    doc: Name of the output file
outputs:
  - id: summary_file
    doc: Summary File in JSON format
    type: File
    outputBinding:
      glob: '*.json'
  - id: logfile
    type: File[]
    outputBinding:
      glob: 'summary*.log'
label: summary
hints:
  - class: DockerRequirement
    dockerPull: lofareosc/prefactor3-cwl
stdout: summary.log
stderr: summary_err.log
$schema:
  - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'