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SNAP Graph as File

SNAP gpt is wrapped as a CWL CommandLineTool with:

class: CommandLineTool
id: sar-calibration
requirements:
  DockerRequirement:
    dockerPull: snap-gpt
  EnvVarRequirement:
    envDef:
      PATH: /srv/conda/envs/env_snap/snap/bin:/usr/share/java/maven/bin:/usr/share/java/maven/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
  ResourceRequirement: {}
baseCommand: gpt
inputs:
  snap_graph:
    inputBinding:
      position: 1
    type: File
  polarization:
    inputBinding:
      position: 2
      prefix: -PselPol=
      separate: false
    type: string
  safe:
    inputBinding:
      position: 2
      prefix: -PinFile=
      separate: false
    type: Directory
outputs:
  results:
    outputBinding:
      glob: .
    type: Directory

cwlVersion: v1.0

This CWL document takes three inputs:

class: CommandLineTool
id: sar-calibration
requirements:
  DockerRequirement:
    dockerPull: snap-gpt
  EnvVarRequirement:
    envDef:
      PATH: /srv/conda/envs/env_snap/snap/bin:/usr/share/java/maven/bin:/usr/share/java/maven/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
  ResourceRequirement: {}
baseCommand: gpt
inputs:
  snap_graph:
    inputBinding:
      position: 1
    type: File
  polarization:
    inputBinding:
      position: 2
      prefix: -PselPol=
      separate: false
    type: string
  safe:
    inputBinding:
      position: 2
      prefix: -PinFile=
      separate: false
    type: Directory
outputs:
  results:
    outputBinding:
      glob: .
    type: Directory

cwlVersion: v1.0

to construct a gpt invocation: 

gpt <snap_graph> -PselPol=<polarization> -PinFile=<safe>

It is a best practice to create a CWL Workflow to wrap the CommandLineTool:

$graph:
- class: Workflow
  id: main
  doc: SNAP Sentinel-1 GRD Calibration
  label: SNAP Sentinel-1 GRD Calibration

  inputs:

    polarization:
      doc: Polarization channel 
      label: Polarization channel 
      type: string

    snap_graph:
      doc: SNAP Graph
      label: SNAP Graph
      type: File

    safe:
      doc: Sentinel-1 GRD product SAFE Directory
      label: Sentinel-1 GRD product SAFE Directory
      type: Directory

  outputs:
  - id: wf_outputs
    outputSource:
    - node_1/results
    type: Directory

  requirements:
    SubworkflowFeatureRequirement: {}

  steps:

    node_1:
      in:
        snap_graph: snap_graph
        polarization: polarization
        safe: safe
      out:
      - results
      run: '#sar-calibration'

- class: CommandLineTool
  id: sar-calibration

  requirements:
    DockerRequirement:
      dockerPull: snap-gpt
    EnvVarRequirement:
      envDef:
        PATH: /srv/conda/envs/env_snap/snap/bin:/usr/share/java/maven/bin:/usr/share/java/maven/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
    ResourceRequirement: {}

  baseCommand: gpt

  inputs:

    snap_graph:
      inputBinding:
        position: 1
      type: File

    polarization:
      inputBinding:
        position: 2
        prefix: -PselPol=
        separate: false
      type: string
    safe:
      inputBinding:
        position: 2
        prefix: -PinFile=
        separate: false
      type: Directory

  outputs:
    results:
      outputBinding:
        glob: .
      type: Directory

  stderr: std.err
  stdout: std.out

cwlVersion: v1.0

The CWL parameters file to run this CWL document contains:

polarization: 'VV'
snap_graph: {class: File, path: ./sar-calibration.xml}
safe: {'class': 'Directory', 'path': './S1A_IW_GRDH_1SDV_20210621T165648_20210621T165713_038441_04893A_EFF6.SAFE'}

Finally, the execution is triggered with:

cwltool sar-calibration-file.cwl sar-calibration-file.yml