add chewtree tool: phylogenetic tree from chewBBACA allele profiles - #1937
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paulzierep wants to merge 3 commits into
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add chewtree tool: phylogenetic tree from chewBBACA allele profiles#1937paulzierep wants to merge 3 commits into
paulzierep wants to merge 3 commits into
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bgruening
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Aug 28, 2026
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| **References** | ||
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| Silva et al. (2018) chewBBACA: A complete suite for gene-by-gene schema creation | ||
| and strain identification. Microbial Genomics. DOI: 10.1099/mgen.0.000166 |
bgruening
reviewed
Aug 28, 2026
| '$phantcec_tree' | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input" format="tsv" type="data" label="chewBBACA allele profile TSV file" help="Tab-separated file with allele calls; first column sample names, subsequent columns loci, last two columns (CC, clonal_complex) excluded"/> |
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| <param name="input" format="tsv" type="data" label="chewBBACA allele profile TSV file" help="Tab-separated file with allele calls; first column sample names, subsequent columns loci, last two columns (CC, clonal_complex) excluded"/> | |
| <param name="input" format="tabular" type="data" label="chewBBACA allele profile TSV file" help="Tab-separated file with allele calls; first column sample names, subsequent columns loci, last two columns (CC, clonal_complex) excluded"/> |
bgruening
reviewed
Aug 28, 2026
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FOR CONTRIBUTOR:
There are two labels that allow to ignore specific (false positive) tool linter errors:
skip-version-check: Use it if only a subset of the tools has been updated in a suite.skip-url-check: Use it if github CI sees 403 errors, but the URLs work.