aoflag.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool
cwlVersion: v1.2
id: aoflagger

baseCommand:
  - aoflagger
inputs:
  - id: msin
    type: Directory[]
    doc: Input measurement set
    inputBinding:
      position: 1
      shellQuote: false
  - id: verbose
    type: boolean?
    doc: will produce verbose output
    inputBinding:
      position: 0
      valueFrom: -v
      shellQuote: false
  - id: n_threads
    type: int?
    doc: |
      overrides the number of threads specified in the strategy
      (default: one thread for each CPU core)
    inputBinding:
      prefix: -j
      position: 0
      shellQuote: false
  - id: strategy
    type:
      - File?
      - string?
    default: '$LINC_DATA_ROOT/rfistrategies/lofar-default.lua'
    doc: |
      specifies a customized strategy
    inputBinding:
      prefix: -strategy
      separate: true
      position: 0
      shellQuote: false

#### READ MODES
  - id: direct_read
    type: boolean?
    doc: |
      Will perform the slowest IO but will always work.
    inputBinding:
      prefix: -direct-read
      position: 0
      shellQuote: false
  - id: reorder
    type: boolean?
    doc: |
      Make aoflagger reorder the measurement set before running the detection.
      This prevents that aoflagger will use its memory reading mode, which is faster but uses more memory.
    inputBinding:
      prefix: -reorder
      position: 0
      shellQuote: false
  - id: memory_read
    type: boolean?
    doc: |
      Will read the entire measurement set in memory. This is the fastest,
      but requires much memory.
    inputBinding:
      prefix: -memory-read
      position: 0