<?xml version="1.0"?>
<!--
# Copyright (C) 2015 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 id="FROGS_clusters_stat" name="FROGS Clusters stat" version="1.4.0">
	<description>Process some metrics on clusters.</description>
 	<requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>
		clusters_stat.py 
		                 --input-biom $biom
		                 --output-file $summary_file
	</command>
	<inputs>
		<param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)." optional="false" />
	</inputs>
	<outputs>
		<data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
	</outputs>
	<tests>
		<test>
			<param name="biom" value="references/04-affiliation.biom"/>
			<output name="summary_file" value="references/05-clustersStat.html" compare="sim_size" delta="0"/>  
		</test>
	</tests>
	<help>

.. image:: static/images/FROGS_logo.png
   :height: 144
   :width: 110


.. class:: infomark page-header h2

What it does

FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ...


.. class:: infomark page-header h2

Input/output

.. class:: h3

Input

**Abundance file**:
 
The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).

The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.

.. class:: h3

Output

**Summary file** (summary.html):

 Clusters metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
 
 *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables

 .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png
    :height: 426
    :width: 520

 .. image:: static/images/FROGS_cluster_stat_clusterDistrib2.png
    :height: 300
    :width: 460
   
 *Sequences distributions* : describes the sequences distribution among clusters

 .. image:: static/images/FROGS_cluster_stat_seq_dist.png
    :height: 326
    :width: 473

 *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering &lt;http://en.wikipedia.org/wiki/Hierarchical_clustering&gt;`_ on samples abundance profile (distance method = `braycurtis &lt;http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis&gt;`_, linkage method = average)

 .. image:: static/images/FROGS_cluster_stat_sample_dist1.png
    :height: 400
    :width: 700

 .. image:: static/images/FROGS_cluster_stat_sample_dist2.png
    :height: 350
    :width: 610

.. class:: infomark page-header h2

Advices

This is a very usefull tool to see the evolution of your OTU. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.


----

**Contact**

Contacts: frogs@inra.fr

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., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_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>