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On CWL

When submitting CWL document(s) to cwl2click, please mind the following constraints:

  • CommandLineTools only will be taken in consideration;
  • The click.Command name is derived from baseCommand and arguments declarations, accepting the patterns below:

both baseCommand and arguments are declared 

baseCommand: runner
arguments:
- crop-cli

baseCommand: 
- runner
arguments:
- crop-cli

baseCommand only is declared:

baseCommand:
- runner
- crop-cli
arguments: []

In all the cases above, the resulting click.Command will result being crop-cli Any other case will force cwl2click not able to detect the command name, then an exception will be thrown.

  • click.Option parameter declaration is derived from inputs[].inputBinding.prefix, i.e.
  - class: CommandLineTool
    id: crop
    baseCommand: 
    - runner
    arguments:
    - crop-cli
    inputs:
      item:
        type: Directory
        inputBinding:
          prefix: --input-item
...

will result to

cli.add_command(
    click.Command(
        name="crop-cli",
        callback=crop_command,
        params=[
            click.Option(
                ["--input-item"],
                "item",
                type=click.Path(path_type=Path, exists=True, readable=True, resolve_path=True, file_okay=False, dir_okay=True),
                multiple=False,
                required=True,
                is_flag=False,

            ),
...

If inputs[].inputBinding.prefix is not found, it will follow up on --{{inputs[].id}}

  • Users have in charge to implement all the callback functions - click2cwl generates the interface only, concrete implementations must be provided by implementors!