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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 38a21bfbbb70a5752ea12898bce9c5601dfcca65"
author | frogs |
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date | Tue, 19 Jul 2022 11:11:16 +0000 |
parents | 445b04a65ed8 |
children | b2967b704d6b |
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<tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> <description>Reconstruction of phylogenetic tree </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="7.407">mafft</requirement> <requirement type="package" version="2.1.9">fasttree</requirement> <requirement type="package" version="4.1.2">r-base</requirement> <requirement type="package" version="4.1">r-essentials</requirement> <requirement type="package" version="2.7.0">r-phangorn</requirement> </expand> <command detect_errors="exit_code"> tree.py --input-sequences '$input_otu' --biom-file '$biomfile' @CPUS@ --out-tree '$out_tree' --html '$html' </command> <inputs> <!-- Files --> <param format="fasta" name="input_otu" type="data" label="Sequence file" help="Sequence file (format: FASTA). Warning: FROGS Tree does not work on more than 10000 sequences!"/> <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance file (format: BIOM)"/> </inputs> <outputs> <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk" /> <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html" /> </outputs> <tests> <test> <param name="input_otu" value="references/09-normalisation.fasta" /> <param name="biomfile" value="references/09-normalisation.biom" /> <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30" /> <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2" /> <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30" /> <output name="html"> <assert_contents> <has_text_matching expression="FROGS\sTree" /> <has_text_matching expression="abundance_removed.*:\s0" /> <has_text_matching expression="abundance_kept.*:\s300" /> <has_text_matching expression="otu_removed.*:\s0" /> <has_text_matching expression="otu_kept.*:\s51" /> </assert_contents> </output> </test> </tests> <help> @HELP_LOGO@ .. class:: infomark page-header h2 What it does This tool creates a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. And creates a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. .. class:: infomark page-header h2 Inputs/Outputs .. class:: h3 Input **Fasta file**: The OTU sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). Careful: FROGS Tree works only with less than 10 000 sequences! .. image:: FROGS_tree_otufile.png **Biom file**: The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). This file can be obtained in particular with the FROGS pipeline. .. class:: h3 Outputs **Newick file** (tree.nwk): The phylogenetic tree in Newick format (format `nwk or nhx <https://en.wikipedia.org/wiki/Newick_format>`_). .. image:: FROGS_nwk_treefile.png **Report file** (report.html): The report file describing which OTUs are contained or not in the phylogenetic tree. .. class:: infomark page-header h2 @HELP_CONTACT@ </help> <expand macro="citations" /> </tool>