[WIP] Update cd-hit to 4.8.1, add cd-hit-454, cd-hit-dup, cd-hit-lap#3328
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stephanflemming wants to merge 20 commits into
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[WIP] Update cd-hit to 4.8.1, add cd-hit-454, cd-hit-dup, cd-hit-lap#3328stephanflemming wants to merge 20 commits into
stephanflemming wants to merge 20 commits into
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Looks really good already.
I guess we should remove https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit once this is merged?
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| <citation type="doi">10.1093/bioinformatics/17.3.282</citation> |
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indentation seems off here... and throughout the file
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| <tool id="cd_hit_454" name="CD-HIT 454" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |||
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please add a recent profile
edam_topics, edam_operations and xrefs would be nice to have as well
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| -M \${GALAXY_MEMORY_MB:-0} |
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Is 0 a useful default?
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What is the state here? Could you fix the conflicts? Once this is in we could also deprecate |
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FOR CONTRIBUTOR:
Update: cd-hit, cd-hit-2d, cd-hit-est, cd-hit-est-2d to 4.8.1
Add: cd-hit-454, cd-hit-dup, cd-hit-lap
This current version of this wrapper (version 4.6.8.1) is not included on usegalaxy.eu, usegalaxy.org and usegalaxy.org.au. But there are multiple old wrappers available
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
https://github.com/galaxyproject/tools-iuc/blob/master/tools/cdhit/cd_hit.xml
https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/
And there is an additional tool for cd-hit outputs: https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ . I am not sure if this is still required and didn't include it here.
There are recipes available for cd-hit and -cd-hit-auxtools. Both are based on the same project repository. Maybe it's a good idea to merge them?
Following subcommands are mentioned in the tool wiki, but skipped here: