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IDBA: fix idba_tran and make testing more rigorous #3150

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merged 2 commits into from Aug 4, 2020
Merged

IDBA: fix idba_tran and make testing more rigorous #3150

merged 2 commits into from Aug 4, 2020

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pvanheus
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@pvanheus pvanheus commented Aug 3, 2020 •
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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)

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pvanheus commented Aug 3, 2020

Two files are changed here:

  1. idba_tran wrapper: this was looking for a scaffold.fa output whereas idba tran produces a contig.fa output. The result was a zero-length output dataset and this was not picked up by the test because it uses sim_size which, by default, means within 10000 bytes. The test dataset is < 1000 bytes so the difference between success and failure was not being noticed.

  2. since the idba_ud wrapper also uses sim_size in its tests, so this was also made more rigorous. The tool version was not bumped because no change to the actual tool was performed.

bernt-matthias
bernt-matthias approved these changes Aug 3, 2020
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tools/idba_ud/idba_ud.xml Outdated
@@ -99,7 +99,7 @@
<has_text text="--min_support 2" />
<has_text text="--seed_kmer 29" />
</assert_command>
<output name="output" file="out/scaffold.fa" compare="sim_size"/>
<output name="output" file="out/scaffold.fa" compare="sim_size" delta="10"/>
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Do we need a delta at all? Maybe even compare="diff" works?

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Yes it does, and switching to "diff" highlighted that the saved output was wrong.

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What is the content of the differing line?

@bgruening bgruening merged commit 665baeb into galaxyproject:master Aug 4, 2020
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@bernt-matthias bernt-matthias bernt-matthias approved these changes

@bgruening bgruening bgruening approved these changes

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@pvanheus @bgruening @bernt-matthias