<?xml version="1.0"?>
<!--
# Copyright (C) 2017 INRA
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# 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
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# This program is distributed in the hope that it will be useful,
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<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.1">
	<description>of samples using different linkage methods</description>
        <requirements>
                <requirement type="package" version="3.1.0">frogs</requirement>
        </requirements>
	<stdio>
		<exit_code range="1:" />
		<exit_code range=":-1" />
	</stdio>
	<command>r_clustering.py 
                                               --html $html 
                                               --rdata $data 
                                               --varExp $varExp 
                                               --distance-matrix $method
	</command>
    <inputs>
		<!-- Files -->
	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
		<!-- Parameters -->	
		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
            <validator type="empty_field" message="This parameter is required." />
        </param>	
	</inputs>
	<outputs>
		<data format="html" name="html" label="${tool.name}: clustering.html" from_work_dir="clustering.html"/>
	</outputs>
	<tests>
		<test>
			<param name="data" value="references/14-phylo_import.Rdata"/>
			<param name="varExp" value="EnvType"/>
			<param name="method" value="references/Unifrac.tsv"/>
			<!--output name="html" file="references/19-phylo_structure.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 contructs the clustering plot for cluster analysis with different linkage methods.


.. class:: infomark page-header h2

Inputs/Outputs

.. class:: h3

Input

**data file** (format RData):
The informations of data in one phyloseq object.
This 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;`_):

.. container:: row

 .. image:: static/images/frogs_images/phyloseq_clustering_ward.png 
   :height: 576
   :width: 768

.. 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>