[FIX] CWL: positional options

[eseiler]

Needs API test patches if it is to be merged

@mr-c @SGSSGene Please check whether this is correct :)

I think:

• Positional options should be required
• Positional list options should be optional (and shown as list)

Here is the CWL from the last test (click)

label: default-index
doc: ""
inputs:
  positional_0:
    doc: this is a positional option.
    type: string
  positional_1:
    doc: "this is a positional option. Default: []"
    type: string[]?
  int:
    doc: "this is a int option. Default: 5"
    type: long?
    inputBinding:
      prefix: --int
  jint:
    doc: this is a required int option.
    type: long
    inputBinding:
      prefix: --jint
  percent:
    doc: this is a required float option.
    type: double
    inputBinding:
      prefix: --percent
  string:
    doc: "this is a string option (advanced). Default: \"\""
    type: string?
    inputBinding:
      prefix: --string
  path01:
    doc: "a normal file. Default: \"\". The input file must exist and read permissions must be granted."
    type: File?
    inputBinding:
      prefix: --path01
  path02:
    doc: "a normal file with a valid file extension. Default: \"\". The input file must exist and read permissions must be granted. Valid file extensions are: [.fa, .fasta]."
    type: File?
    inputBinding:
      prefix: --path02
  path03:
    doc: "a input directory. Default: \"\". An existing, readable path for the input directory."
    type: Directory?
    inputBinding:
      prefix: --path03
  path04:
    doc: "a output file. Default: \"\". The output file must not exist already and write permissions must be granted."
    type: string?
    inputBinding:
      prefix: --path04
  path05:
    doc: "a output directory. Default: \"\". A valid path for the output directory."
    type: string?
    inputBinding:
      prefix: --path05
  flag:
    doc: this is a flag.
    type: boolean?
  kflag:
    doc: this is a flag.
    type: boolean?
outputs:
  path04:
    type: File?
    outputBinding:
      glob: $(inputs.path04)
  path05:
    type: Directory?
    outputBinding:
      glob: $(inputs.path05)
cwlVersion: v1.2
class: CommandLineTool
baseCommand:
  - format_cwl_test
  - index

$ cwltool --validate test.cwl
test.cwl:45:3: object id `test.cwl#path04` previously defined
test.cwl:50:3: object id `test.cwl#path05` previously defined
test.cwl is valid CWL.

path04 and path05 occur in both input and output. I'm not sure if this is a warning or just a note by the cwltool?

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Name	Status	Preview	Updated (UTC)
sharg-parser	✅ Ready (Inspect)	Visit Preview	Feb 14, 2024 11:36am

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (3b55514) 91.94% compared to head (fb246f5) 92.01%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #237      +/-   ##
==========================================
+ Coverage   91.94%   92.01%   +0.07%     
==========================================
  Files          17       17              
  Lines        1627     1629       +2     
==========================================
+ Hits         1496     1499       +3     
+ Misses        131      130       -1     

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[SGSSGene]

Looks good! Thank you

[SGSSGene]

The CWL warning is not beautiful, but was there before and should be fixed in TDL at some point.