--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_beta_diversity.xml	Thu Feb 28 10:14:49 2019 -0500
@@ -0,0 +1,145 @@
+<?xml version="1.0"?>
+<!--
+# 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 Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.1">
+	<description>distance matrix</description>
+        <requirements>
+                <requirement type="package" version="3.1.0">frogs</requirement>
+        </requirements>
+	<stdio>
+		<exit_code range="1:" />
+		<exit_code range=":-1" />
+	</stdio>
+	<command>r_beta_diversity.py 
+                                        --rdata $data
+                                        --varExp $varExp
+                                        #if $methods != "None"
+                                            #if $other_method != ""
+                                                --distance-methods $methods,$other_method
+                                            #else
+                                                --distance-methods $methods
+                                            #end if
+                                        #else
+                                            #if $other_method != ""
+                                                --distance-methods $other_method
+                                            #end if
+                                        #end if
+                                        --matrix-outdir BetaMatrix
+                                        --html $html
+	</command>
+    <inputs>
+		<!-- Files -->
+	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+		<!-- Parameters -->	
+        <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="methods" type="select" label="The methods of beta diversity" help="N.B. if the tree is not available in your RData, you cannot choose Unifrac or Weighted Unifrac" multiple="true" display="checkboxes">
+            <option value="unifrac" selected="False">Unifrac</option>
+            <option value="wunifrac" selected="False">Weighted Unifrac</option>
+            <option value="bray" selected="False">Bray-Curtis</option>
+            <option value="cc" selected="False">Jaccard</option>
+        </param>
+        <param type="text" name="other_method" label="Other method" help="The other methods of beta diversity that you want to use (comma separated value). c.f. details below." optional="false" value="" size="40"/>
+    </inputs>
+	<outputs>
+        <data format="html" name="html" label="${tool.name}: beta_diversity" from_work_dir="beta_diversity.html">
+            <discover_datasets pattern="__designation__" ext="tabular" directory="BetaMatrix" visible="true"/>
+        </data>
+	</outputs>
+        <tests>
+                <test>
+                        <param name="data" value="references/14-phylo_import.Rdata" />
+                        <param name="varExp" value="EnvType" />
+                        <param name="methods" value="cc,unifrac" />
+                        <!--output name="html" file="references/17-phylo_beta_div.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 compute beta distance matrix and display them in a heatmap
+
+
+.. 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 phylogenetic tree, and the sample experiment metadata.
+This file is the result of "FROGS Phyloseq Import Data tool".
+
+**distance methods** :
+The list of Phyloseq distanceMethodList is available here `distanceMethodList &lt;https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf&gt;`_ .
+You have to copy the exact name as in this list in the parameter window "Other Method".
+To use several methods, separate them by a space.
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
+
+The review of beta diversity with heatmap plots:
+
+.. image:: static/images/frogs_images/phyloseq_beta_diversity.png 
+     :height: 609
+     :width: 800 
+
+
+**beta diversity matrix** (format tabular):
+The distance matrix of beta diversity.
+
+ .. image:: static/images/frogs_images/phyloseq_beta_diversity_matrix.png 
+
+.. 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>