[MISC] Allow recursive subcommands

[eseiler]

After

• [MISC] Defer everything to parse() #238
• [MISC] Use vector for arguments #239
• [MISC] Check that parse was not called #240
• [MISC] Allow options for subcommands #244

I kinda forgot about this one :)

[mr-c]

What does this do to the CWL export?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.12%. Comparing base (7534545) to head (ef1d6f5).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #233      +/-   ##
==========================================
+ Coverage   95.10%   95.12%   +0.01%     
==========================================
  Files          18       18              
  Lines        1735     1742       +7     
==========================================
+ Hits         1650     1657       +7     
  Misses         85       85              

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[eseiler]

What does this do to the CWL export?

CTD looks ok, CWL has a duplicate base command?

Click to open

/path/to/app remote set-url --export-help {ctd,cwl}

<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" name="git-remote-set-url">
    <executableName><![CDATA[/path/to/app]]></executableName>
    <citations />
    <PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
        <NODE name="remote" description="" tags="basecommand">
            <NODE name="set-url" description="" tags="basecommand">
                <ITEM name="positional_0" value="" type="string" description="" required="false" advanced="false" />
            </NODE>
        </NODE>
    </PARAMETERS>
</tool>

label: git-remote-set-url
doc: ""
inputs:
  []
outputs:
  []
cwlVersion: v1.2
class: CommandLineTool
baseCommand:
  - app
  - remote
  - set-url
  - set-url

[mr-c]

I'd like to see a test to confirm sane CWL output

[eseiler]

I'd like to see a test to confirm sane CWL output

This'll need deNBI-cibi/tool_description_lib#50 #235

Might be a follow-up PR to add a test.
As far as I can tell, only the baseCommand isn't handled correctly.

[seqan-actions]

Documentation preview available at https://docs.seqan.de/preview/seqan/sharg-parser/233

CWL test added

[SGSSGene]

Nice! Looks good to me!