Parameter References

Overview

Teaching: 10 min
Exercises: 0 min
Questions
  • How do I reference input parameters in other fields?

Objectives
  • Learn how to make parameter references in descriptions.

In a previous example, we extracted a file using the “tar” program. However, that example was very limited because it assumed that the file we were interested in was called “hello.txt”. In this example, you will see how to reference the value of input parameters dynamically from other fields.

tar-param.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [tar, xf]
inputs:
  tarfile:
    type: File
    inputBinding:
      position: 1
  extractfile:
    type: string
    inputBinding:
      position: 2
outputs:
  example_out:
    type: File
    outputBinding:
      glob: $(inputs.extractfile)

tar-param-job.yml

tarfile:
  class: File
  path: hello.tar
extractfile: goodbye.txt

Create your input files and invoke cwl-runner with the tool wrapper and the input object on the command line:

$ rm hello.tar || true && touch goodbye.txt && tar -cvf hello.tar goodbye.txt
$ cwl-runner tar-param.cwl tar-param-job.yml
[job tar-param.cwl] /tmp/tmpwH4ouT$ tar \
    xf \
    /tmp/tmpREYiEt/stgd7764383-99c9-4848-af51-7c2d6e5527d9/hello.tar \
    goodbye.txt
[job tar-param.cwl] completed success
{
    "example_out": {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "basename": "goodbye.txt",
        "nameroot": "goodbye",
        "nameext": ".txt",
        "location": "file:///home/me/cwl/user_guide/goodbye.txt",
        "path": "/home/me/cwl/user_guide/goodbye.txt",
        "class": "File",
        "size": 0
    }
}
Final process status is success

Certain fields permit parameter references which are enclosed in $(...). These are evaluated and replaced with value being referenced.

outputs:
  example_out:
    type: File
    outputBinding:
      glob: $(inputs.extractfile)

References are written using a subset of Javascript syntax. In this example, $(inputs.extractfile), $(inputs["extractfile"]), and $(inputs['extractfile']) are equivalent.

The value of the “inputs” variable is the input object provided when the CWL tool was invoked.

Note that because File parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write $(inputs.tarfile.path).

Where are parameter references allowed?

You can only use parameter references in certain fields. These are:

Key Points

  • Some fields permit parameter references enclosed in $(...).

  • References are written using a subset of Javascript syntax.