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r_beta_diversity.xml
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r_beta_diversity.xml
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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 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: [email protected]
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>