| Previous changeset 0:f0601c1f41b6 (2016-06-16) |
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Commit message:
Deleted selected files |
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removed:
affiliation_OTU.xml |
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| 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 |
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| @@ -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 <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> |