# HG changeset patch
# User maille
# Date 1466083395 14400
# Node ID 43b9bf4bc44c8d36edad0aa8597da6551cb550ea
# Parent  f0601c1f41b69cf8af103caccddc1de9f3f4f7a9
Deleted selected files

diff -r f0601c1f41b6 -r 43b9bf4bc44c affiliation_OTU.xml
--- a/affiliation_OTU.xml	Thu Jun 16 09:21:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-<?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>