# HG changeset patch
# User maille
# Date 1466083280 14400
# Node ID f0601c1f41b69cf8af103caccddc1de9f3f4f7a9

Uploaded

diff -r 000000000000 -r f0601c1f41b6 affiliation_OTU.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/affiliation_OTU.xml	Thu Jun 16 09:21:20 2016 -0400
@@ -0,0 +1,150 @@
+<?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_affiliation_OTU" name="FROGS Affiliation OTU" version="0.7.0">
+	<description>Step 4 in metagenomics analysis : Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description>
+	<command interpreter="python2.7">
+		affiliation_OTU.py 
+		                       --reference $ref_file
+		                       --input-biom $biom_abundance 
+		                       --input-fasta $fasta_sequences
+		                       --output-biom $biom_affiliation 
+		                       --summary $summary 
+		                       --nb-cpus $nb_cpu 
+		                       --java-mem $mem
+	</command>
+	<inputs>
+		<!-- JOB Parameter -->
+		<param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param>
+		<param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param>
+		<!-- Database Choice -->
+		<param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">
+       		<options from_file="frogs_db.loc">
+          		<column name="name" index="0"/>
+          		<column name="value" index="1"/>
+       		</options>
+   		</param> 
+        <!-- Files -->
+        <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/>
+        <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/>
+	</inputs>
+	<outputs>
+		<data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation.biom" from_work_dir="affiliation.biom" />
+		<data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/>
+	</outputs>
+  	<help>
+
+.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png 
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Add taxonomic affiliation in abundance file.
+
+
+.. class:: infomark page-header h2
+
+Inputs/outputs
+
+.. class:: h3
+
+Inputs
+
+**Sequence file**:
+
+The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file**:
+ 
+The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file** (tax_affiliation.biom):
+
+ The abundance file with affiliation (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Summary file** (report.html):
+
+ This file presents the number of sequences affiliated by blast, and the number of multi-affiliation (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
+ 
+ .. image:: ${static_path}/images/tools/frogs/FROGS_affiliation_summary.png 
+    :height: 800
+    :width: 600
+
+
+.. class:: infomark page-header h2
+
+Reference database
+
+The databases come from `SILVA &lt;http://www.arb-silva.de/&gt;`_ a comprehensive and quality checked rRNA database.
+
+FROGS database(s) pre-process:
+
+1. The non-redondant small sub-unit database is retrieved from SILVA.
+
+2. This database is processed to keep only the taxonomy level: Domain - Phylum - Class - Order - Family - Genus - Species
+
+3. The database is splitted in two databses: prokaryote and eukaryote.
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+.. csv-table:: 
+   :header: "Steps", "Description"
+   :widths: 5, 150
+   :class: table table-striped
+
+   "1", "`RDPClassifier &lt;https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html&gt;`_ is used with database to associate to each OTU a taxonomy and a bootstrap (example: *Bacteria;(1.0);Firmicutes;(1.0);Clostridia;(1.0);Clostridiales;(1.0);Clostridiaceae 1;(1.0);Clostridium sensu stricto;(1.0);*)."
+   "2", "`blastn+ &lt;http://blast.ncbi.nlm.nih.gov/&gt;`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score has reported."
+   "3", "For each OTU with several blastn+ results a consensus is determined on each taxonomic level. If all the taxa in a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. By example, if you have an OTU with two corresponding sequences, the first is a *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, the second is a *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*."
+
+
+.. class:: infomark page-header h2
+
+Advices
+
+This tool can take large time. It is recommended to filter your abundance and your sequence file before this tool (see **FROGS Filters**).
+
+As you can see the affiliation of each OTU is not human readable in outputed abundance file. We provide a tools to convert these BIOM file in tabulated file, see the **FROGS BIOM to TSV** tool.
+
+
+----
+
+**Contact**
+
+Contacts: frogs@toulouse.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., 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">10.1186/1471-2105-10-421</citation>
+		<citation type="doi">10.1128/AEM.00062-07</citation>
+	</citations>
+</tool>