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Exclusive parameters in a workflow

I've implemented a CommandLineTool that has exclusive parameters

inputs: 
  touchparam:
    type:
      - type: record
        name: touchcode
        fields: 
          touchcode:
            type: string 
            inputBinding:
              position: 1
      - type: record
        name: touchfile
        fields:
          touchfile:
            type: File
            inputBinding:
              prefix: -f

but I can't quite get the syntax to bind the inputs from a workflow:

steps:
  generate:
    run: Generate.cwl
    in: []
    out: [rannum]

  touch:
    run: Touch.cwl
    in: 
      touchparam:
        touchfile: generate/rannum
    out: [results]

This was just a guess based on how you bind them from a yml file. Any help?

cwl
• 1,652 views • link
written by pete.hague • pete.hague

Thanks for the answer

It looks like the workflow you've implemented there takes the exclusive parameter as an input to itself, which is not what I am intending.

The second step is the one with the exclusive parameter, although it always takes the same one from the previous step. The full workflow and tool files are here:

https://github.com/petehague/Stoa/blob/master/actions/workflow1.cwl https://github.com/petehague/Stoa/blob/master/actions/Generate.cwl https://github.com/petehague/Stoa/blob/master/actions/Touch.cwl

For this test case, the workflow itself should not take any inputs.

• 1 views • link
written by pete.hague • pete.hague

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under the answer below.

• 1 views • link
written by GenoMax GenoMax

3 answers

I implemented a solution based on my reading of what you have done:

First, the tool:

cwlVersion: v1.0
class: CommandLineTool

inputs: 
  touchparam:
    type:
      - type: record
        name: touchcode
        fields: 
          touchcode:
            type: string 
            inputBinding:
              position: 1
      - type: record
        name: touchfile
        fields:
          touchfile:
            type: File
            inputBinding:
              prefix: -f

stdout: my_output.txt

outputs:
  out:
    type: stdout

baseCommand: echo

with a workflow:

cwlVersion: v1.0
class: Workflow
inputs:
  touchit:
   type:
    - type: record
      name: touchcode
      fields:
        touchcode: 
          type: string
    - type: record
      name: touchfile
      fields:
        touchfile:
          type: File

outputs:
  out:
   type: File
   outputSource: step1/out

steps:
  step1:
    run: tool/tool.cwl
    in:
      touchparam: touchit
    out: [out]

and then two input files, first a string input:

touchparam:
  touchcode: "foo"

and then a file input:

touchit:
  touchfile:
    class: File
    path: my_output.txt

I hope this helps!

• 1 views • link
written by Peter vH Peter vH

Peter vH : If the two answers below are duplicates then please delete them.

• 1 views • link
written by GenoMax GenoMax

I implemented a solution based on my reading of what you have done:

First, the tool:

cwlVersion: v1.0
class: CommandLineTool

inputs: 
  touchparam:
    type:
      - type: record
        name: touchcode
        fields: 
          touchcode:
            type: string 
            inputBinding:
              position: 1
      - type: record
        name: touchfile
        fields:
          touchfile:
            type: File
            inputBinding:
              prefix: -f

stdout: my_output.txt

outputs:
  out:
    type: stdout

baseCommand: echo

with a workflow:

cwlVersion: v1.0
class: Workflow
inputs:
  touchit:
   type:
    - type: record
      name: touchcode
      fields:
        touchcode: 
          type: string
    - type: record
      name: touchfile
      fields:
        touchfile:
          type: File

outputs:
  out:
   type: File
   outputSource: step1/out

steps:
  step1:
    run: tool/tool.cwl
    in:
      touchparam: touchit
    out: [out]

and then two input files, first a string input:

touchparam:
  touchcode: "foo"

and then a file input:

touchit:
  touchfile:
    class: File
    path: my_output.txt

I hope this helps!

• 0 views • link
written by Peter vH Peter vH

I implemented a solution based on my reading of what you have done:

First, the tool:

cwlVersion: v1.0
class: CommandLineTool

inputs: 
  touchparam:
    type:
      - type: record
        name: touchcode
        fields: 
          touchcode:
            type: string 
            inputBinding:
              position: 1
      - type: record
        name: touchfile
        fields:
          touchfile:
            type: File
            inputBinding:
              prefix: -f

stdout: my_output.txt

outputs:
  out:
    type: stdout

baseCommand: echo

with a workflow:

cwlVersion: v1.0
class: Workflow
inputs:
  touchit:
   type:
    - type: record
      name: touchcode
      fields:
        touchcode: 
          type: string
    - type: record
      name: touchfile
      fields:
        touchfile:
          type: File

outputs:
  out:
   type: File
   outputSource: step1/out

steps:
  step1:
    run: tool/tool.cwl
    in:
      touchparam: touchit
    out: [out]

and then two input files, first a string input:

touchparam:
  touchcode: "foo"

and then a file input:

touchit:
  touchfile:
    class: File
    path: my_output.txt

I hope this helps!

• 0 views • link
written by Peter vH Peter vH

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