Mercurial > repos > frogs > frogs_2_0_0
diff tree.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
| author | frogs |
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| date | Thu, 25 Oct 2018 05:01:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tree.xml Thu Oct 25 05:01:13 2018 -0400 @@ -0,0 +1,137 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_Tree" name="FROGS Tree" version="1.0.0"> + <description>Reconstruction of phylogenetic tree </description> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>tree.py + --input-otu $input_otu + #if $template.fileTemplate + --template-pynast ${template.template_pynast} + #end if + --biomfile $biomfile + --nb-cpus $nb_cpus + --out-tree $out_tree + --html $html + </command> + <inputs> + <!-- Files --> + <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <conditional name="template"> + <param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" /> + <when value="false"></when> + <when value="true"> + <param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" /> + </when> + </conditional> + <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameter --> + <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" /> + </inputs> + <outputs> + <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/> + <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="input_otu" value="references/04-filters.fasta"/> + <conditional name="template"> + <param name="fileTemplate" value="false"/> + </conditional> + <param name="biomfile" value="references/04-affiliation.biom"/> + <output name="out_tree" value="references/10b-tree.nwk"/> + </test> + </tests> + <help> +.. image:: static/images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Creation of a multiple alignment of OTUs with `PyNAST <http://biocore.github.io/pynast/>`_ (if you have an alignment template file) or with `Mafft <http://mafft.cbrc.jp/alignment/software>`_ (if you have not an aligned template file). +And creation of a phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**OTUs fasta file**: + +The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). +Careful: FROGS Tree works only with less than 10 000 sequences! + + .. image:: static/images/frogs_tree_otufile.png + +**(optional) Template alignment file**: + +A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement <https://en.wikipedia.org/wiki/Multiple_sequence_alignment>`_). + + .. image:: static/images/frogs_tree_templatefile.png + +**OTUs 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 `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). + + .. image:: static/images/nwk_treefile.png + +**Html file** (summary.html): + +The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + </help> + <citations> + <citation type="doi">10.7287/peerj.preprints.386v1</citation> + </citations> +</tool>