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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Fix cut tool #1448

Open bernt-matthias opened 1 week ago

bernt-matthias commented 1 week ago

the list of columns must be after -f (or -c i.e. cut_element). I would have liked to add a test, but we can not use an option with the value "," in a test (it will split it to a list of options ["", ""]).

Still broken is that data_column parameters do not work for anything besides tab and comma separated values. Fixing this properly would require a restructuring of the tool form....

bgruening commented 1 week ago

Its unfortunately not a suite, so every change will bump all tools. So better to increase all versions?

bernt-matthias commented 1 week ago

Its unfortunately not a suite, so every change will bump all tools. So better to increase all versions?

In this case we might consider fixing cut properly. Wondering how to structure the tool form in the best way. The point is that data_column will only work for tab and comma separated inputs (i.e. on the choice of infile (format) and delimiter).

bgruening commented 1 week ago

For which inputs is this a problem? Is the real fix here to make the tool form more flexible and allow an overwrite in those cases?

bernt-matthias commented 1 week ago

If we choose anything but tab or comma in the delimiter the tool is broken at the moment, because data_column only works for tabular input data (with columns metadata), which is only defined for csv, tsv and tabular.