shellQuote value as input parameter

CWL Questions
1

I would like to specify “shellQuote” in CommandLineBinding as false or true depending on cwl input.

inputs:
  use_shellQuote:
    type: boolean

  reference_genome: 
    type: File
    secondaryFiles: [.fai]
    inputBinding:
      shellQuote: $(inputs.use_shellQuote)

I get an error message:

shellQuote` field
  is not valid because
    tried
    boolean but
      the
      value is not boolean

Unfortunately it is not possible to use expression in shellQuote field - only boolean is possible. How to solve this problem?

2

Hi @Monika_Krzyzanowska, could you describe what are you trying to do?

3

Hi Monika,

All input information is evaluated at the same time, which means that one input cannot use the information of another input.

I would like to understand more of what you are doing, but one alternative might be to use arguments which are evaluated after inputs.

i.e

inputs:
  # Should I use 'shellQuote' for reference genome input
  use_shellQuote:
    type: boolean

  # Reference genome input see 'arguments' for inputBinding logic
  reference_genome:
    type: File
    secondaryFiles: 
      - .fai

arguments:
  - position: 100 # 100 for after all other inputs (use -1 if you wish to place item before all inputs)
    valueFrom: $(inputs.reference_genome.path)
    shellQuote: $(inputs.use_shellQuote)
4

This isn’t right, you have to use valueFrom: $(inputs.reference_genome.path). @Monika_Krzyzanowska’s question is specifically about parameterizing shellQuote, which is not possible. But without knowing what she’s actually trying to accomplish I can’t give an alternate solution.

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