Mercurial > repos > frogs > frogs_3_1_0
diff r_beta_diversity.xml @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
| author | frogs |
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| date | Thu, 28 Feb 2019 10:14:49 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_beta_diversity.xml Thu Feb 28 10:14:49 2019 -0500 @@ -0,0 +1,145 @@ +<?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 Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.1"> + <description>distance matrix</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_beta_diversity.py + --rdata $data + --varExp $varExp + #if $methods != "None" + #if $other_method != "" + --distance-methods $methods,$other_method + #else + --distance-methods $methods + #end if + #else + #if $other_method != "" + --distance-methods $other_method + #end if + #end if + --matrix-outdir BetaMatrix + --html $html + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="methods" type="select" label="The methods of beta diversity" help="N.B. if the tree is not available in your RData, you cannot choose Unifrac or Weighted Unifrac" multiple="true" display="checkboxes"> + <option value="unifrac" selected="False">Unifrac</option> + <option value="wunifrac" selected="False">Weighted Unifrac</option> + <option value="bray" selected="False">Bray-Curtis</option> + <option value="cc" selected="False">Jaccard</option> + </param> + <param type="text" name="other_method" label="Other method" help="The other methods of beta diversity that you want to use (comma separated value). c.f. details below." optional="false" value="" size="40"/> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: beta_diversity" from_work_dir="beta_diversity.html"> + <discover_datasets pattern="__designation__" ext="tabular" directory="BetaMatrix" visible="true"/> + </data> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="methods" value="cc,unifrac" /> + <!--output name="html" file="references/17-phylo_beta_div.html" compare="sim_size" delta="0" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" /> + </assert_contents> + </output> + </test> + </tests> + + <help> + +.. image:: static/images/frogs_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 compute beta distance matrix and display them in a heatmap + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +One phyloseq object containing OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +This file is the result of "FROGS Phyloseq Import Data tool". + +**distance methods** : +The list of Phyloseq distanceMethodList is available here `distanceMethodList <https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf>`_ . +You have to copy the exact name as in this list in the parameter window "Other Method". +To use several methods, separate them by a space. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +The review of beta diversity with heatmap plots: + +.. image:: static/images/frogs_images/phyloseq_beta_diversity.png + :height: 609 + :width: 800 + + +**beta diversity matrix** (format tabular): +The distance matrix of beta diversity. + + .. image:: static/images/frogs_images/phyloseq_beta_diversity_matrix.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool>