Mercurial > repos > frogs > frogs_2_0_0
diff affiliation_OTU.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
| author | frogs |
|---|---|
| date | Thu, 25 Oct 2018 05:01:13 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affiliation_OTU.xml Thu Oct 25 05:01:13 2018 -0400 @@ -0,0 +1,169 @@ +<?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="0.8.0"> + <description>Step 4 in metagenomics analysis : Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + #set $reference_fasta_filename = str( $ref_file.fields.path ) + affiliation_OTU.py + --reference "${reference_fasta_filename}" + --input-biom $biom_abundance + --input-fasta $fasta_sequences + --output-biom $biom_affiliation + --summary $summary + --nb-cpus $nb_cpu + --java-mem $mem + #if $rdp + --rdp + #end if + </command> + <inputs> + <!-- JOB Parameter --> + <param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param> + <param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param> + <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> + <options from_data_table="frogs_db"></options> + <validator type="no_options" message="A built-in database is not available" /> + </param> + <param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" /> + <!-- Files --> + <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/> + <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/> + </inputs> + <outputs> + <data format="biom1" name="biom_affiliation" label="${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> + <tests> + <test> + <param name="ref_file" value="db"/> + <param name="fasta_sequences" value="swarm.fasta"/> + <param name="biom_abundance" value="swarm.biom"/> + <output name="biom_affiliation" file="references/Blast_affiliation.biom"/> + <output name="summary" file="references/Blast_affiliation.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 + +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/images/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@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>