--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_structure.xml	Thu Oct 25 05:01:13 2018 -0400
@@ -0,0 +1,131 @@
+<?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 Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="1.0.0">
+	<description>with heatmap plot and ordination 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_structure.py 
+                                         --html $html
+                                         --rdata $data
+                                         --varExp $varExp
+                                         --ordination-method $method
+                                         --distance-matrix $distance
+	</command>
+    <inputs>
+		<!-- Files -->
+	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data Tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+		<!-- Parameters -->	
+		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+		<param name="method" type="select" label="Ordination method">
+			<option value="MDS" >MDS/PCoA</option>
+			<option value="NMDS" >NMDS</option>
+            <option value="DPCoA" >DPCoA</option>
+        </param>
+	</inputs>
+	<outputs>
+		<data format="html" name="html" label="${tool.name}: structure.html" from_work_dir="structure.html"/>
+	</outputs>
+        <tests>
+                <test>
+                        <param name="data" value="references/11-phylo_import.Rdata" />
+                        <param name="varExp" value="EnvType" />
+                        <param name="method" value="MDS" />
+                        <param name="distance" value="references/Unifrac.tsv" />
+                        <!--output name="html" file="references/15-phylo_structure.html" compare="sim_size" delta="10" /-->
+	                <output name="html">
+                                <assert_contents>
+                                        <has_text_matching expression="html\sxmlns=.*" />
+                                        <has_text_matching expression="application/json.*DesLardons" />
+                                </assert_contents>
+                        </output>
+
+                </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 heatmap plot and ordination plot with the `ordination methods &lt;https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods&gt;`_ to visualise data structure.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format rdata):
+The informations of data in one phyloseq object.
+This file is the result of "FROGS Phyloseq Import Data tool".
+
+**distance file** (format tabular):
+The data file containing beta diversity distance matrix.
+This file is the result of "FROGS Phyloseq Beta Diversity tool".
+
+.. class:: h3
+
+Output
+
+**html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
+
+The review of data structure with an ordination plot and with an heatmap plot:
+
+.. image:: static/images/phyloseq_plot_sample_ellipse.png 
+     :height: 343
+     :width: 450
+
+.. image:: static/images/phyloseq_plot_heatmap_red.png 
+     :height: 343
+     :width: 450
+
+.. class:: infomark page-header h2
+
+**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., 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>