[WIP] Update cd-hit to 4.8.1, add cd-hit-454, cd-hit-dup, cd-hit-lap

[stephanflemming]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

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

• cd-hit-dup
• cd-hit-auxtools, 0.5-2012-03-07-fix-dan-gh-0.0.1
• Nov 10, 2015

https://github.com/galaxyproject/tools-iuc/blob/master/tools/cdhit/cd_hit.xml

• cd-hit, cd-hit-est, cd-hit-2d, cd-hit-est-2d
• cd-hit, 4.6.8
• Oct 15, 2018

https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/

• cd-hit, cd-hit-est
• cd-hit, 4.6.4
• May 4, 2018

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?

• https://github.com/weizhongli/cdhit
• Conda recipe cd-hit: https://bioconda.github.io/recipes/cd-hit/README.html
• Conda recipe auxtools: https://bioconda.github.io/recipes/cd-hit-auxtools/README.html

Following subcommands are mentioned in the tool wiki, but skipped here:

• cd-hit-clstr_2_blm8: running, no output
• cd-hit-clstr_2_blm8.pl: running, no output
• cd-hit-div: not needed in Galaxy
• cd-hit-div.pl: see cd-hit-div
• cd-hit-otu: not running
• cd-hit-para.pl: not longer supported, since the multi-threaded cd-hit become available
• cd-hit-2d-para.pl: not longer supported, since the multi-threaded cd-hit become available
• h-cd-hit: not running
• psi-cd-hit: not running

[bernt-matthias]

Looks really good already.

I guess we should remove https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit once this is merged?

[bernt-matthias]

indentation seems off here... and throughout the file

[bernt-matthias]

please add a recent profile

edam_topics, edam_operations and xrefs would be nice to have as well

[bernt-matthias]

Is 0 a useful default?

[bernt-matthias]

I think we need set -eo pipefail

[bernt-matthias]

What is the state here? Could you fix the conflicts?

Once this is in we could also deprecate cd-hit-dup in the devteam repo (xref galaxyproject/tools-devteam#616)