<?xml version="1.0" encoding="UTF-8"?>
<!--
# 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.
#
# 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="FROGSSTAT_Phyloseq_Alpha_Diversity" name="FROGSSTAT Phyloseq Alpha Diversity" version="@TOOL_VERSION@+galaxy2">
	<description>with richness plot</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements_phyloseq" />

	<stdio>
		<exit_code range="1:" />
		<exit_code range=":-1" />
	</stdio>
	<command>phyloseq_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.nb.html" from_work_dir="alpha_diversity.nb.html"/>
	</outputs>
    <tests>
        <test>
            <param name="data" value="references/16-phylo_import.Rdata" />
            <param name="varExp" value="EnvType" />
            <param name="measures" value="Observed,Chao1,Shannon" />
            <output name="alphaD" file="references/18-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
            <!-- <output name="html" value="references/18-phylo_alpha_div.nb.html" compare="diff" lines_diff="0"/> -->
            <output name="html">
                <assert_contents>
                    <!-- check anova on Observed alpha metrics -->
                    <has_text text='EnvType      7  18148    2593   5.383 9.78e-05' />
                    <!-- check anova on Chao1 alpha metrics -->
                    <has_text text='EnvType      7  13764    1966   2.492   0.0269' />
                    <!-- check anova on Chao1 alpha metrics -->
                    <has_text text='EnvType      7 11.333   1.619   3.553 0.003209' />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

@HELP_LOGO@

.. 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/FROGS_Phyloseq_plot_richness.png
     :height: 400
     :width: 525

.. image:: static/images/FROGS_Phyloseq_plot_richness_box.png
     :height: 400
     :width: 499

.. image:: static/images/FROGS_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/FROGS_Phyloseq_alpha_diversity_table.png

.. class:: infomark page-header h2

@HELP_CONTACT@

	</help>

    <citations>
        <expand macro="citations" />
    </citations>
    
</tool>