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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Fix invalid datatypes #4009

Open bernt-matthias opened 3 years ago

bernt-matthias commented 3 years ago

IUC has quite some tools using datatypes that are not known to Galaxy:

for i in $(grep 'format="' . --include "*xml" -r | sed "s/'/\"/g" | sed 's/.*format="\([^"]*\)".*/\1/' | sed 's/,/\n/g' | sort -u) 
do
if ! grep -q "\"$i\"" ~/projects/galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample;
then
echo "- $i" && grep "format=\"$i" . --include "*xml" -r -l | sort -u | sed 's/^/  - /'
fi
done | grep -E -v "\.gz|\.bz2"

Would be cool to extend planemo lint checking for valid datatypes, but I could not find datatypes.conf (or the sample) in any of the galaxy-* packages. Comments for this are very welcome.

bernt-matthias commented 3 years ago

Would be cool to extend planemo lint checking for valid datatypes

This might come automatically (but via planemo test) by https://github.com/galaxyproject/galaxy/pull/12073

bernt-matthias commented 3 years ago

Would be cool to extend planemo lint checking for valid datatypes

This might come automatically (but via planemo test) by galaxyproject/galaxy#12073

True for inputs that are covered by tests. But not for uncovered inputs and all outputs. So linting for this would be cool.