CWL: Make Enum optional (CommandInputEnumSchema)
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6.5 years ago
eduardo ▴ 10

Is it possible to make an Enum optional?

  outfmt:
      type:
          type: enum
          symbols:
            - clustal
            - clustal_num
            - fa
            - msf
            - nexus
            - phylip
            - selex
            - stockholm
            - vienna
          inputBinding:
            position: 13
            prefix: --outfmt

I have tried enum? but then it is not recognised as CommandInputEnumSchema.

cwl • 2.7k views
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1
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? is just a shorthand for [ <T>, "null"]. Try the latter.

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Could you provide an example? I have tried a few alternatives with null but I couldn't make it work.

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Any idea on how to make the enum an array?

The following breaks:

type:
  - "null"
  - type: enum[]

The only way I found is custom type as the example mentioned by Michael R. Crusoe

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/master/tools/InterProScan5.21-60.cwl#L38

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type:
  - "null"
  - type: array
    items:
      type: enum
      symbols: [none, apply, calculate]

Yes, as you found, it is easier when we give names to our custom types

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Awesome! Thank you very much!

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