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SRST2 has incorrect format on discover datasets outputs. #6459

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hexylena opened this issue Oct 16, 2024 · 3 comments
Open

SRST2 has incorrect format on discover datasets outputs. #6459

hexylena opened this issue Oct 16, 2024 · 3 comments

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@hexylena
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hexylena commented Oct 16, 2024

$ ag discover_datasets.*format.*,
tools/srst2/srst2.xml
200:            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/>

srst2 is the only tool to use a format with a , which seems incorrect, as the file gets marked 'binary or unknown' in galaxy even though it's a plain old tabular file.

For me the results are tabular but I'm not very familiar with this tool so I'm guessing that txt was there for a reason.

@bernt-matthias perhaps this is something that should be linted against? The XSD does not have a problem with a comma there (or maybe the case where a format has a comma in the name is permitted? though that would be confusing.)

@hexylena
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@EngyNasr I see you're the author of this wrapper, did you experience txt outputs from srst2?

@bernt-matthias
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Et voila: galaxyproject/galaxy#17600 .. maybe we get it with 24.2 :)

@hexylena
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Incredible work @bernt-matthias !

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