command line input specification using custom enum not working unless they are arrays

[esanzgar]

When a custom type is defined elsewhere and it is used on a CommandLineTool, the custom type has to be used as an array. Otherwise, cwltool can't make a command line argument from it.

Expected Behavior

$cwltool https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl --help

usage: https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl
       [-h] [job_order]

positional arguments:
  job_order   Job input json file

optional arguments:
  -h, --help  show this help message and exit
  **--applications APPLICATIONS**

Actual Behavior

--application option is not present:

$cwltool https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl --help

usage: https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl
       [-h] [job_order]

positional arguments:
  job_order   Job input json file

optional arguments:
  -h, --help  show this help message and exit

Workflow Code

https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl

Debug

cwltool --debug https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl --help

**Can't make command line argument from https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/MyTypes.yaml#opt**

usage: https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/custom-types.cwl
       [-h] [job_order]

positional arguments:
  job_order   Job input json file

optional arguments:
  -h, --help  show this help message and exit

Your Environment

• cwltool version: 1.0.20170928192020

[mr-c]

• add a test for this

Code location: https://github.com/common-workflow-language/cwltool/blob/master/cwltool/main.py#L412