Update chewbbaca with manual species ID

[nilchia]

The species ID is not static and changes over time.

This update makes it users resposibility to check the correct species ID.

Fixes: #7868

I'll open another PR later and also update the tool version.

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

There are two labels that allow to ignore specific (false positive) tool linter errors:

• skip-version-check: Use it if only a subset of the tools has been updated in a suite.
• skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

[wm75]

I assume this should become a conditional for the next two parameters?

[nilchia]

True. added here e6b3f94

[wm75]

Seems like the correct thing to do, yes 👍

[nilchia]

I think it is good to go

[bernt-matthias]

Please report this upstream. A species identifier that does not identify seems wrong and super user unfriendly. Maybe suggest to use taxids?

Do the IDs depend on used reference data? Does the user know how to find the correct IDs?

[nilchia]

Yes it is really user unfriendly.

Yes users can run NSSTATS.xml tool to get list of available species in the database.

Also other thing is that the tool is not reproducible if the IDs change.

[nilchia]

ping: @pavanvidem 480d9cb

[nilchia]

Did adding "unzip" cause that error?

[pavanvidem]

Did adding "unzip" cause that error?

No, it is coming from plotly

Job in error state.. tool_id: chewbbaca_extractcgmlst, exit_code: 1, stderr: Traceback (most recent call last):
  File "/usr/local/bin/chewBBACA.py", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/usr/local/lib/python3.11/site-packages/CHEWBBACA/chewBBACA.py", line 1543, in main
    functions_info[process][1]()
  File "/usr/local/lib/python3.11/site-packages/CHEWBBACA/utils/process_datetime.py", line 146, in wrapper
    func(*args, **kwargs)
  File "/usr/local/lib/python3.11/site-packages/CHEWBBACA/chewBBACA.py", line 810, in run_determine_cgmlst
    determine_cgmlst.main(**vars(args))
  File "/usr/local/lib/python3.11/site-packages/CHEWBBACA/ExtractCgMLST/determine_cgmlst.py", line 365, in main
    fig.update_xaxes(range=[0, len(sorted_genomes)],
  File "/usr/local/lib/python3.11/site-packages/plotly/graph_objs/_figure.py", line 23508, in update_xaxes
    obj.update(patch, overwrite=overwrite, **kwargs)
  File "/usr/local/lib/python3.11/site-packages/plotly/basedatatypes.py", line 5195, in update
    BaseFigure._perform_update(self, kwargs, overwrite=overwrite)
  File "/usr/local/lib/python3.11/site-packages/plotly/basedatatypes.py", line 3949, in _perform_update
    raise err
ValueError: Invalid property specified for object of type plotly.graph_objs.layout.XAxis: 'titlefont'

Did you mean "tickfont"?