Enhance relabel_from_file to work with any column pair in mapping file

[wm75]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

This can save a cut step in WFs.
Will provide tests if you think it's useful.

[jmchilton]

I don't use Galaxy or follow the latest trends in tool design - so feel free to just dismiss this suggestion if it doesn't reflect how tools are actually used. My gut is though I would implement this as changing:

                <option value="txt">Using lines in a simple text file.</option>
                <option value="tabular">Map original identifiers to new ones using a two column table.</option>

to:

                <option value="txt">Using lines in a simple text file.</option>
                <option value="tabular">Map original identifiers to new ones using the first two columns of a simple table.</option>
                <option value="tabular_configured">Map original identifiers to new ones using arbitrary columns from a table.</option>

And then adding more advanced option in that new selection when - including like comment line skipping and table type options (stuff like break on commas instead of tabs). But that might be overkill.

Either way though - this seems solid and I'm a +1 on it after it has tests and the linting issue is fixed.

[wm75]

And then adding more advanced option in that new selection when - including like comment line skipping and table type options (stuff like break on commas instead of tabs). But that might be overkill.

I hadn't considered such advanced options because, so far, I've only encountered the column issue during WF development.
Now your comment made me think of https://github.com/galaxyproject/iwc/tree/main/workflows/data-fetching/sra-manifest-to-concatenated-fastqs. @lldelisle I seem to remember there was an issue with that one initially about the SRA run data file being csv instead of tab-separated? I think the current patch would already allow simplification of the current WF, but maybe check if there is a missed opportunity for even more here.

[lldelisle]

Hi everyone,
Not sure this would help in this workflow as I need to create a new column anyway...
But this is generally speaking a really good idea.