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<?xml version="1.0" encoding="UTF-8"?>
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# Copyright (C) 2017 INRA
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<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="1.0.0">
	<description>with richness 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_alpha_diversity.py
                                             --rdata $data 
                                             --varExp $varExp
                                             --alpha-measures $measures
                                             --alpha-out $alphaD 
                                             --html $html
	</command>
    <inputs>
		<!-- Files -->
	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
		<!-- Parameters -->	
		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
            <validator type="empty_field" message="This parameter is required." />
        </param>        
	    <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
             <option value="Observed" selected="True">Observed</option>
             <option value="Chao1" selected="True">Chao1</option>
             <option value="Shannon" selected="True">Shannon</option>
             <option value="InvSimpson" selected="True">InvSimpson</option>
             <option value="Simpson">Simpson</option>
             <option value="ACE">ACE</option>
             <option value="Fisher">Fisher</option>
        </param>
	</inputs>
	<outputs>
		<data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
		<data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/>
	</outputs>
        <tests>
                <test>
                        <param name="data" value="references/11-phylo_import.Rdata" />
                        <param name="varExp" value="EnvType" />
                        <param name="measures" value="Observed,Chao1,Shannon" />
                        <output name="alphaD" file="references/13-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
                </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 richness plots to visualise sample alpha diversity.

.. 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 phylogenetics tree, and the sample experiment metadata.
This file is the result of "FROGS Phyloseq Import Data tool".

.. class:: h3

Output

**Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): the review of richness plots and rarefaction curves.

.. image:: static/images/phyloseq_plot_richness.png 
     :height: 400
     :width: 525 

.. image:: static/images/phyloseq_plot_richness_box.png
     :height: 400
     :width: 499
     
.. image:: static/images/phyloseq_rarefaction_curves.png
     :height: 400
     :width: 498

**Alpha diversity table** (alpha_diversity.tsv):
The data file containing table of alpha diversity indices.

.. image:: static/images/phyloseq_alpha_diversity_table.png

.. 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>