diff clusters_stat.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/clusters_stat.xml	Thu Oct 25 05:01:13 2018 -0400
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+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 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="FROGS_clusters_stat" name="FROGS Clusters stat" version="1.4.0">
+	<description>Process some metrics on clusters.</description>
+ 	<requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+	<command>
+		clusters_stat.py 
+		                 --input-biom $biom
+		                 --output-file $summary_file
+	</command>
+	<inputs>
+		<param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)." optional="false" />
+	</inputs>
+	<outputs>
+		<data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="biom" value="references/04-affiliation.biom"/>
+			<output name="summary_file" value="references/05-clustersStat.html" compare="sim_size" delta="0"/>  
+		</test>
+	</tests>
+	<help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ...
+
+
+.. class:: infomark page-header h2
+
+Input/output
+
+.. class:: h3
+
+Input
+
+**Abundance file**:
+ 
+The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
+
+.. class:: h3
+
+Output
+
+**Summary file** (summary.html):
+
+ Clusters metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
+ 
+ *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables
+
+ .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png
+    :height: 426
+    :width: 520
+
+ .. image:: static/images/FROGS_cluster_stat_clusterDistrib2.png
+    :height: 300
+    :width: 460
+   
+ *Sequences distributions* : describes the sequences distribution among clusters
+
+ .. image:: static/images/FROGS_cluster_stat_seq_dist.png
+    :height: 326
+    :width: 473
+
+ *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering &lt;http://en.wikipedia.org/wiki/Hierarchical_clustering&gt;`_ on samples abundance profile (distance method = `braycurtis &lt;http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis&gt;`_, linkage method = average)
+
+ .. image:: static/images/FROGS_cluster_stat_sample_dist1.png
+    :height: 400
+    :width: 700
+
+ .. image:: static/images/FROGS_cluster_stat_sample_dist2.png
+    :height: 350
+    :width: 610
+
+.. class:: infomark page-header h2
+
+Advices
+
+This is a very usefull tool to see the evolution of your OTU. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.
+
+
+----
+
+**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., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_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>