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Split meryl #5942

Merged
merged 11 commits into from
Apr 25, 2024
Merged

Split meryl #5942

merged 11 commits into from
Apr 25, 2024

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bernt-matthias
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@bernt-matthias bernt-matthias commented Apr 9, 2024

Created a little script to split Galaxy tools covering subparsers (since I needed it elsewhere). Should cover inputs, outputs, command, tests, tool id and name.

No idea:

  • should we deprecate the original tool?
  • should we create a suite from this? Otherwise this will be the meryl repo containing the splited new tools.

Maybe someone else wants to split the help and description ... because this can not be automated.

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)

@natefoo
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natefoo commented Apr 9, 2024

Thank you for this!

I guess we should maybe update the descriptions? Also the help can be trimmed down for each function.

@bgruening
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The shed.yml needs to be ported to a suite one.

generated using reformat.sh from bbmap

reformat.sh in=test-data/child.fasta out=test-data/child.fastq qfake=40 fastareadlen=150 qout=33 addcolon=t trimreaddescription=t uniquenames=t
to stay in size limits
- add assumptions of meryldb zip files
- output names
@@ -0,0 +1,123 @@
<tool id="meryl_arithmetic_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
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higher profile version?

@bgruening bgruening merged commit a95f5b0 into galaxyproject:main Apr 25, 2024
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3 participants