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neo417 wants to merge 4 commits into from
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Add PhyloPhlAn tool #1639

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79192f6
Add PhyloPhlAn tool
neo417 Jun 16, 2025
8ab61ce
Fix version suffix token
neo417 Jun 16, 2025
b47b589
Fix tool shed categories
neo417 Jun 16, 2025
638aabb
Fix linting issue
neo417 Jun 16, 2025
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10 changes: 10 additions & 0 deletions tools/phylophlan/.shed.yml
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name: phylophan
owner: bgruening
description: Tool for high-resolution phylogenetic analysis and taxonomic classification of microbial genomes and MAGs.
homepage_url: https://github.com/biobakery/phylophlan
long_description: PhyloPhlAn is a comprehensive and scalable pipeline for phylogenetic profiling of microbial genomes and metagenomes. It supports accurate species- and strain-level classification, including for metagenome-assembled genomes (MAGs), and can reconstruct large-scale phylogenies using clade-specific informative markers.
remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/phylophlan
categories:
- Metagenomics
- Sequence Analysis
- Phylogenetics
102 changes: 102 additions & 0 deletions tools/phylophlan/macros.xml
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<macros>
<token name="@TOOL_VERSION@">3.1.1</token>
<token name="@VERSION_SUFFIX@">0</token>

<!-- Requirements -->
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">phylophlan</requirement>
<yield/>
<!-- phylophlan uses python disutils which was removed in python 3.12 -->
<requirement type="package" version="3.11">python</requirement>
</requirements>
</xml>
<xml name="requirements_phylophlan">
<expand macro="requirements">
<requirement type="package" version="2.1.11">diamond</requirement>
<requirement type="package" version="2.16.0">blast</requirement>
<requirement type="package" version="12.0">usearch</requirement>
<requirement type="package" version="5.3">muscle</requirement>
<requirement type="package" version="7.526">mafft</requirement>
<requirement type="package" version="2.1.10">fasttree</requirement>
<requirement type="package" version="8.2.12">raxml</requirement>
<requirement type="package" version="2.4.0">iqtree</requirement>
<requirement type="package" version="5.7.8">astral-tree</requirement>
</expand>
</xml>
<xml name="requirements_assign_sgbs">
<expand macro="requirements">
<requirement type="package" version="2.3">mash</requirement>
</expand>
</xml>

<!-- PhyloPhlAn input blocks -->
<xml name="config_select_software">
<conditional name="db">
<param name="type" type="select" argument="-d / -t" label="Database marker type">
<option value="n">Nucleotides</option>
<option value="a">Amino acids</option>
</param>
<when value="n">
<param argument="--db_dna" type="select" label="Nucleotide database">
<option value="makeblastdb">makeblastdb</option>
</param>
<param argument="--map_dna" type="select" label="Map genomes using">
<option value="blastn">blastn</option>
<option value="tblastn">tblastn</option>
<option value="diamond">diamond</option>
</param>
</when>
<when value="a">
<param argument="--db_aa" type="select" label="Amino acid database">
<option value="diamond">diamond</option>
<option value="usearch">usearch</option>
</param>
<param argument="--map_aa" type="select" label="Map proteomes using">
<option value="diamond">diamond</option>
<option value="usearch">usearch</option>
</param>
<param argument="--map_dna" type="select" optional="true" label="Map genomes using">
<option value="diamond">diamond</option>
<option value="blastn">blastn</option>
<option value="tblastn">tblastn</option>
</param>
</when>
</conditional>
<param argument="--msa" type="select" label="Multiple-sequence alignment">
<option value="mafft">mafft</option>
<option value="muscle">muscle</option>
<!-- <option value="opal">opal</option> -->
<!-- <option value="upp">upp</option> -->
</param>
<yield/>
</xml>
<xml name="config_supertree_maas">
<!-- WARNING! PhyloPhlAn sends the second column of the file to raxml via the command line. -->
<conditional name="maas">
<param name="source" type="select" label="Substitution models"
help="A mapping file that specifies the RAxML substitution model to use for each specific marker for gene tree reconstruction. &lt;br&gt;This file must be present for every Supertree analysis, but is only used if raxml is selected for --gene_trees1/2. Otherwise you can ignore the parameter. &lt;br&gt;The included file lists the substitution models for each of the 400 universal markers of the PhyloPhlAn database.">
<option value="default">Included PhyloPhlAn models file</option>
<option value="history">From History</option>
</param>
<when value="default"/>
<when value="history">
<param name="models" type="data" format="tabular" label="Substitution models"
help="The file should be a mapping from amino acid markers to their respective (raxml) substitution model. It should be a two-columns file separated by TAB, where the first column specifies the name of the marker and the second the name of the substitution model to use. e.g. &lt;br&gt;p0000 PROTCATLG&lt;br&gt;...&lt;br&gt;p0004 PROTCATLG&lt;br&gt;p0005 PROTCATCPREVF"/>
</when>
</conditional>
</xml>

<!-- Misc -->
<xml name="biotools">
<xrefs>
<xref type="bio.tools">PhyloPhlAn</xref>
</xrefs>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1038/s41467-020-16366-7</citation>
<yield/>
</citations>
</xml>
</macros>
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