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author | frogs |
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date | Thu, 25 Oct 2018 05:01:13 -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_remove_chimera" name="FROGS Remove chimera" version="1.3.0"> <description>Step 3 in metagenomics analysis : Remove PCR chimera in each sample.</description> <requirements> <requirement type="package" version="2.0.1">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <command> remove_chimera.py --nb-cpus $nb_cpus --input-fasta $sequence_file --non-chimera $non_chimera_fasta --summary $summary_file #if $abundance_type.abundance_type_selected == "biom" --input-biom $abundance_biom --out-abundance $out_abundance_biom #else --input-count $abundance_count --out-abundance $out_abundance_count #end if </command> <inputs> <!-- Files --> <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" /> <conditional name="abundance_type"> <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored."> <option value="biom" selected="true">BIOM file</option> <option value="count">TSV file</option> </param> <when value="biom"> <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" /> </when> <when value="count"> <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" /> </when> </conditional> <!-- Parameters --> <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" /> <!-- <param name="size_separator" type="text" label="Size separator" help="Fill this input only if the IDs of sequences in fasta store the abundance as suffix. Example: 'Cluster_1;size=10' => ';size='" value="" optional="true" /> --> </inputs> <outputs> <data format="fasta" name="non_chimera_fasta" label="${tool.name}: non_chimera.fasta" from_work_dir="non_chimera.fasta"/> <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom"> <filter>abundance_type['abundance_type_selected'] == "biom"</filter> </data> <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv"> <filter>abundance_type['abundance_type_selected'] == "count"</filter> </data> <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> </outputs> <tests> <test> <param name="sequence_file" value="references/02-clustering.fasta"/> <conditional name="abundance_type"> <param name="abundance_type_selected" value="biom"/> <param name="abundance_biom" value="references/02-clustering.biom" /> </conditional> <output name="non_chimera_fasta" file="references/03-chimera.fasta"/> </test> </tests> <help> .. image:: static/images/FROGS_logo.png :height: 144 :width: 110 .. class:: infomark page-header h2 What it does Remove chimeric sequences by sample. .. class:: infomark page-header h2 Context Chimeras are sequences formed from two or more biological sequences joined together. The majority of these anomalous sequences are formed from an incomplete extension during a PCR cycle. During subsequent cycles, a partially extended strand can bind to a template derived from a different but similar sequence. This phenomena is particularly common in amplicon sequencing where closely related sequences are amplified. .. 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 cluster in each sample (format `BIOM <http://biom-format.org/>`_). OR The abundance of each sequence in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). This type of file is produced by *FROGS pre-process*. Example:: #id splA splB seq1 1289 2901 seq2 3415 0 .. class:: h3 Outputs **Sequence file** (non_chimera.fasta): The sequence file with only non-chimera (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). **Abundance file** (non_chimera.biom or non_chimera.tsv): The abundance file with only non-chimera (format the same of the abundance input). **Summary file** (report.html): This file presents the number of removed elements (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). .. class:: infomark page-header h2 How it works .. csv-table:: :header: "Steps", "Description" :widths: 10, 90 :class: table table-striped "1", "Split input data by sample (classicaly the PCR is realised by sample)." "2", "Find chimera in each sample (`vsearch <https://github.com/torognes/vsearch>`_)." "3", "Remove the sequences identify as chimera in all samples where they are present." ---- **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">10.7287/peerj.preprints.386v1</citation> </citations> </tool>