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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.
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# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-->
<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 &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods &lt;https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):

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: [e-mail]

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>