<?xml version="1.0"?>
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# Copyright (C) 2017 INRA
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# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
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<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 &lt;https://joey711.github.io/phyloseq/&gt;`_ 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 &lt;https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf&gt;`_ .
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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):

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>