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date | Thu, 16 Jun 2016 09:21:20 -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_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 <https://en.wikipedia.org/wiki/FASTA_format>`_). **Abundance file**: The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). .. class:: h3 Outputs **Abundance file** (tax_affiliation.biom): The abundance file with affiliation (format `BIOM <http://biom-format.org/>`_). **Summary file** (report.html): This file presents the number of sequences affiliated by blast, and the number of multi-affiliation (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). .. 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 <http://www.arb-silva.de/>`_ 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 <https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html>`_ 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+ <http://blast.ncbi.nlm.nih.gov/>`_ 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>