diff r_clustering.xml @ 0:76c750c5f0d1 draft default tip

planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_clustering.xml	Thu Oct 25 05:01:13 2018 -0400
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+<?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 Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="1.0.0">
+	<description>of samples using different linkage methods</description>
+	<requirements>
+		<requirement type="package" version="2.0.1">frogs</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+		<exit_code range=":-1" />
+	</stdio>
+	<command>r_clustering.py 
+                                               --html $html 
+                                               --rdata $data 
+                                               --varExp $varExp 
+                                               --distance-matrix $method
+	</command>
+    <inputs>
+		<!-- Files -->
+	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+		<!-- Parameters -->	
+		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>	
+	</inputs>
+	<outputs>
+		<data format="html" name="html" label="${tool.name}: clustering.html" from_work_dir="clustering.html"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="data" value="references/11-phylo_import.Rdata"/>
+			<param name="varExp" value="EnvType"/>
+			<param name="method" value="references/Unifrac.tsv"/>
+			<!--output name="html" file="references/16-phylo_structure.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_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 contructs the clustering plot for cluster analysis with different linkage methods.
+
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**data file** (format RData):
+The informations of data in one phyloseq object.
+This 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;`_):
+
+.. container:: row
+
+ .. image:: static/images/phyloseq_clustering_ward.png 
+   :height: 576
+   :width: 768
+
+.. 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>