Set tool output format string from workflow inputs

CWL Questions
4

This example didn’t quite work, but it led me to a working example (with the help of examples such as Input of array of enum is not recognized by the cwltool command line input object feature · Issue #576 · common-workflow-language/cwltool · GitHub):

  output_path_format:
    label: Format for output file
    doc: |-
      Format for the output file
      Type: string
      Accepted values:
        - for pdb files:
          https://edamontology.org/format_1476
        - for mol2 files:
          https://edamontology.org/format_3816
      Default value: https://edamontology.org/format_1476 (for default system.pdb file)
    type:
      - string
      - type: array
        items:
          type: enum
          symbols:
            - edam:format_1476
            - edam:format_3816
    default: https://edamontology.org/format_1476

I’ve included a default value - but found that cwltool doesn’t seem to use the namespace for expanding this, so have had to enter it explicitly.

$namespaces:
  edam: https://edamontology.org/