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Add bio.tools IDs to tool wrappers #616

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Add bio.tools IDs to tool wrappers #616

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supernord
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Adding multiple bio.tools IDs as part of BioHackathon 2023 project 25

nsoranzo
nsoranzo reviewed Nov 1, 2023
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tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml
@@ -3,6 +3,9 @@
<requirements>
<requirement type="package" version="1.0.0">taxonomy</requirement>
</requirements>
<xrefs>
<xref type="bio.tools">gi2taxonomy</xref>
</xrefs>
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I think this tool should be moved to deprecated instead, it doesn't seem to be installed on big 3 servers and its requirement is not installable any more (no conda package, sources on BitBucket removed).

nsoranzo
nsoranzo reviewed Nov 1, 2023
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...multispecies_orthologous_microsats/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml
@@ -1,5 +1,8 @@
<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.0">
<description> for multiple (>2) species alignments</description>
<xrefs>
<xref type="bio.tools">multispecies_orthologous_microsats</xref>
</xrefs>
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This tool also should probably be moved to deprecated/.

@supernord
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@nsoranzo - should this one be deprecated as well? https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/rRNA/rRNA_prediction.xml

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nsoranzo commented Nov 3, 2023

@nsoranzo - should this one be deprecated as well? https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/rRNA/rRNA_prediction.xml

I think so, @bgruening what do you think?

@bgruening
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Yes. Thanks @supernord

@supernord
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Should the following also be deprecated?

@bernt-matthias
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How to continue here?

@bernt-matthias
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Should the following also be deprecated

Depends .. could you tell us the reasons for each of these cases?

@bernt-matthias bernt-matthias mentioned this pull request Mar 13, 2024
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@supernord @nsoranzo @bgruening @bernt-matthias