Add HyPhy CLN tool wrapper #7626
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- Implements `hyphy cln` for cleaning and normalizing alignments. - Supports filtering duplicates, gap-only sites, and masking stop codons. - Adds regression test `test-data/cln-stop-codons.fa`.
SaimMomin12
reviewed
Jan 28, 2026
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Some minor comments. Could we also get rid of the .lint_skip file of the tool suite?
Additionally, some of the tests fail.
tools/hyphy/hyphy_cln.xml
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| <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: Cleaned alignment" /> | ||
| </outputs> | ||
| <tests> | ||
| <test> |
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Suggested change
| <test> | |
| <test expect_num_outputs="1"> |
tools/hyphy/hyphy_cln.xml
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| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test> |
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| <test> | |
| <test expect_num_outputs="1"> |
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important to note, this now bumps hyphy to 2.5.93 (and consequently tidy up some test data to satisfy stricter data sanity reqs in newer hyphy). that was the only reasonable way to fix the hyphy cln test failure. |
bgruening
reviewed
Feb 9, 2026
tools/hyphy/hyphy_sm19.xml
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| year = "1989", | ||
| note = "Genetics 123(3):603-613", | ||
| url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"} | ||
| url = "https://doi.org/10.1093/genetics/123.3.603"} |
Update hyphy_sm19.xml
bgruening
approved these changes
Feb 10, 2026
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Danke! |
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Deployment status: success https://github.com/galaxyproject/tools-iuc/actions/runs/21862922360 |
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hyphy clnfor cleaning and normalizing alignments.test-data/cln-stop-codons.fa.FOR CONTRIBUTOR: