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Issues when mapping Galaxy toolshed to bio.tools #1821

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fbacall opened this issue Apr 10, 2024 · 4 comments
Closed

Issues when mapping Galaxy toolshed to bio.tools #1821

fbacall opened this issue Apr 10, 2024 · 4 comments

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@fbacall
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fbacall commented Apr 10, 2024

Spaces in tool name:

          {
            "value": "GA4GH Beacon",
            "reftype": "bio.tools"
          }

...the actual bio.tools ID is GA4GH_Beacon

Comma-separated tools:

          {
            "value": "graphclust, GraphClust2",
            "reftype": "bio.tools"
          }

...graphclust and GraphClust2 are both valid bio.tools ID, so we need to link the Galaxy tool to multiple bio.tools entries

fbacall added a commit that referenced this issue Apr 10, 2024
handle tool IDs with spaces in name. #1821
@supernord
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hey @fbacall
the first one is a metadata issue - if you haven't already, I can generate a PR against that tool wrapper with the fix?

@fbacall
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fbacall commented Apr 11, 2024

hey @fbacall the first one is a metadata issue - if you haven't already, I can generate a PR against that tool wrapper with the fix?

Sounds good!

@hexylena
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The second one is also definitely an issue, we've started linting that they're valid identifiers, that's not valid as far as galaxy is concerned. The wrapper should be fixed there too

@supernord
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galaxyproject/tools-iuc#5951

@fbacall fbacall closed this as completed May 14, 2024
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