Mercurial > repos > frogs > frogs_2_0_0
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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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<?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 name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="1.0.0"> <description>from 3 files: biomfile, samplefile, treefile </description> <requirements> <requirement type="package" version="2.0.1">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <command>r_import_data.py --biomfile $biomfile #if $samplefile --samplefile $samplefile #end if --treefile $treefile --ranks "$ranks" #if $normalization --normalization #end if --html $html --rdata $data </command> <inputs> <!-- Files --> <param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the OTU informations (format: biom1)." optional="false"> <validator type="empty_field" message="This parameter is required." /> </param> <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false"> <validator type="empty_field" message="This parameter is required." /> </param> <param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" /> <!-- Parameters --> <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space." value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/> <param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> </inputs> <outputs> <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/> <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> </outputs> <tests> <test> <param name="biomfile" value="references/chaillou.biom"/> <param name="samplefile" value="references/sample_metadata.tsv"/> <param name="treefile" value="references/tree.nwk"/> <output name="data" value="references/11-phylo_import.Rdata"/> </test> </tests> <help> .. image:: static/images/FROGS_logo.png :height: 144 :width: 110 .. class:: infomark page-header h2 What it does Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq <https://joey711.github.io/phyloseq/>`_ object. .. class:: infomark page-header h2 Inputs/Outputs .. class:: h3 Input **OTU biom file**: The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). This file is the result of FROGS BIOM to std BIOM. The example of biom file: .. image:: static/images/biomfile.png :height: 30 :width: 733 **Newick file** (tree.nwk): Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: .. image:: static/images/nwk_treefile.png **Sample file**: The file contains the conditions of experiment with sample ID in the first column: .. image:: static/images/phyloseq_samplefile.png :height: 115 :width: 369 .. class:: h3 Output **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. .. image:: static/images/phyloseq_import_data_html.png **Data file** (format rdata): The informations of data in one phyloseq object. .. 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>