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Adds the chewtree tool (split out from the vienna_rna update commit) for building phylogenetic trees from chewBBACA allele profiles.
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Should we combine the two Python scripts into one? |
| python '$__tool_directory__/scripts/mentalist_tree.py' '$phantcec_dm' > '$phantcec_tree' | ||
| ]]></command> | ||
| <inputs> | ||
| <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"/> |
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ChewBBACA allelcall output is a collection. Probably it is better if this tool also accepted input as a collection
| <param name="input_type" type="select" label="Input matrix type"> | ||
| <option value="allele" selected="true">Allele profile - calculate Hamming distance matrix</option> | ||
| <option value="distance">Distance matrix - use pre-computed distance matrix directly</option> | ||
| </param> |
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Can the dm be calculated from other tools?
If it is only calculated here, then the input should be only the allele profile.
| description: Builds phylogenetic trees from allelic profiles using ChewBBACA | ||
| homepage_url: https://github.com/B-UMMI/ChewBBACA | ||
| long_description: | | ||
| ChewTree is part of the ChewBBACA suite. It builds phylogenetic trees from allelic profiles computed by ChewBBACA's AlleleCall algorithm. |
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| ChewTree is part of the ChewBBACA suite. It builds phylogenetic trees from allelic profiles computed by ChewBBACA's AlleleCall algorithm. | |
| ChewTree is part of the Galaxy ChewBBACA tool suite. It builds phylogenetic trees from allelic profiles computed by ChewBBACA's AlleleCall algorithm. |
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For me it sounded like it is part of the tool upstream.
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mh, I can add this ... but this raises a new question. Should we move this tool into the chewbbaca folder under IUC?
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I don't even know where those scripts are coming from. @paulzierep ?
Do you, @nilchia, know if those are part of chewbacca upstream somewhere?
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I also don't know where they are from.
But I know they are not part of ChewBBACA upstream code
Co-authored-by: Amirhossein Nilchi <66441226+nilchia@users.noreply.github.com>
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https://github.com/bgruening/cgmlst_filtering_and_clustering/blob/main/README.md Actually this is the one you shared with me before. |
2 participants
closes #1937
Adds the chewtree tool (split out from the vienna_rna update commit) for building phylogenetic trees from chewBBACA allele profiles.
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.