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summary.cwl 3.30 KiB
class: CommandLineTool
cwlVersion: v1.2
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
id: summary
baseCommand:
- make_summary.py
inputs:
- id: flagFiles
type:
- File[]
- File
inputBinding:
position: 1
doc: List of files with flag information (JSON)
- id: pipeline
type: string?
default: 'LINC'
inputBinding:
position: 0
prefix: --pipeline
doc: Name of the pipeline
- id: run_type
default: 'calibrator'
type: string?
inputBinding:
position: 0
prefix: --run_type
doc: Type of the pipeline
- id: filter
default: '*&'
type: string?
inputBinding:
position: 0
prefix: --filtered_antennas
doc: Filter these antenna string from the processing.
- id: bad_antennas
default: '*&'
type: string?
inputBinding:
position: 0
prefix: --bad_antennas
doc: Antenna string to be processed
- id: structure_file
default: false
type:
- boolean?
- File?
inputBinding:
position: 0
prefix: --structure_file
- id: Ateam_separation_file
default: false
type:
- boolean?
- File?
inputBinding:
position: 0
prefix: --Ateam_separation_file
- id: solutions
default: false
type:
- boolean?
- File?
inputBinding:
position: 0
prefix: --solutions
- id: clip_sources
default: false
type: - string?
- boolean?
inputBinding:
position: 0
prefix: --clip_sources
separate: true
itemSeparator: ','
valueFrom: '$(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: string?
inputBinding:
position: 0
prefix: --demix
shellQuote: false
separate: 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
- id: ionex
default: false
type:
- string?
- boolean?
inputBinding:
position: 0
prefix: --ionex
separate: true itemSeparator: ','
valueFrom: '$(self)'
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: astronrd/linc
stdout: summary.log
stderr: summary_err.log
$schema:
- 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'