view r_alpha_diversity.xml @ 0:59bc96331073 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647

<?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 name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.1">
	<description>with richness plot</description>
        <requirements>
                <requirement type="package" version="3.1.0">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/14-phylo_import.Rdata" />
                <param name="varExp" value="EnvType" />
                <param name="measures" value="Observed,Chao1,Shannon" />
                <output name="alphaD" file="references/16-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
            </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 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_images/phyloseq_plot_richness.png 
     :height: 400
     :width: 525 

.. image:: static/images/frogs_images/phyloseq_plot_richness_box.png
     :height: 400
     :width: 499
     
.. image:: static/images/frogs_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/frogs_images/phyloseq_alpha_diversity_table.png

.. class:: infomark page-header h2

**Contact**

Contacts: [e-mail]

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>