Mercurial > repos > frogs > frogs_2_0_0
diff r_structure.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/r_structure.xml Thu Oct 25 05:01:13 2018 -0400 @@ -0,0 +1,131 @@ +<?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 Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="1.0.0"> + <description>with heatmap plot and ordination plot</description> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_structure.py + --html $html + --rdata $data + --varExp $varExp + --ordination-method $method + --distance-matrix $distance + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data Tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="method" type="select" label="Ordination method"> + <option value="MDS" >MDS/PCoA</option> + <option value="NMDS" >NMDS</option> + <option value="DPCoA" >DPCoA</option> + </param> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: structure.html" from_work_dir="structure.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/11-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="method" value="MDS" /> + <param name="distance" value="references/Unifrac.tsv" /> + <!--output name="html" file="references/15-phylo_structure.html" compare="sim_size" delta="10" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="application/json.*DesLardons" /> + </assert_contents> + </output> + + </test> + </tests> + <help> + +.. image:: static/images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods <https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods>`_ to visualise data structure. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format rdata): +The informations of data in one phyloseq object. +This file is the result of "FROGS Phyloseq Import Data tool". + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of "FROGS Phyloseq Beta Diversity tool". + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +The review of data structure with an ordination plot and with an heatmap plot: + +.. image:: static/images/phyloseq_plot_sample_ellipse.png + :height: 343 + :width: 450 + +.. image:: static/images/phyloseq_plot_heatmap_red.png + :height: 343 + :width: 450 + +.. 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>