Mercurial > repos > jbrayet > annotatepeaks
changeset 0:9f656b0bfe88 draft
Uploaded
author | jbrayet |
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date | Thu, 13 Aug 2015 11:01:52 -0400 |
parents | |
children | 69aa94839d0f |
files | annotatePeaks_wrapper.xml |
diffstat | 1 files changed, 152 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotatePeaks_wrapper.xml Thu Aug 13 11:01:52 2015 -0400 @@ -0,0 +1,152 @@ +<!--annotatePeaks - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr> +Copyright (C) 2015 Institut Curie + +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="annotatePeaks" name="AnnotatePeaks" version="1.0"> + <description>Genomic annotation of Chip-Seq peaks</description> + <requirements> + <requirement type="package" version="2.11.1">fontconfig</requirement> + <requirement type="package" version="3.1.2">R</requirement> + </requirements> + <command interpreter="bash"> +#if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotatePeaks_wrapper.sh -f $inputfile -y $log -m $minScore -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -y $log -c $controlfile -x $statsControl -o $outputPNG -m $minScore -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotatePeaks_wrapper.sh -y $log -f $inputfile -e $regfile -m $minScore -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -c $controlfile -x $statsControl -l $left -y $log -o $outputPNG -m $minScore -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotatePeaks_wrapper.sh -f $inputfile -y $log -m $minScore -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -y $log -c $controlfile -x $statsControl -o $outputPDF -m $minScore -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotatePeaks_wrapper.sh -y $log -f $inputfile -e $regfile -m $minScore -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotatePeaks_wrapper.sh -f $inputfile -c $controlfile -x $statsControl -l $left -y $log -o $outputPDF -m $minScore -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 1#end if + </command> + <inputs> + + <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/> + <param name="minScore" type="float" label="MinimalScore" value="0" help="Set to 0 if you don't want to filter your .BED file with peaks"/> + + <conditional name="use_control"> + <param name="use_control_selector" type="select" label="Use control data"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/> + </when> + </conditional> + + <param name="left" type="integer" label="Define Promoter is a region up to X bp upstream gene TSS" value="-2000"/> + <param name="right" type="integer" label="Define Immediate Downstream is a region up to X bp downstream gene TSS" value="2000"/> + <param name="EnhLeft" type="integer" label="Define Enhancer is a region up to X bp upstream gene TSS" value="-30000"/> + <param name="DownGene" type="integer" label="Define Gene Downstream is a region up to X bp downstream transcription end" value="5000"/> + + +<conditional name="input_organism"> + <param name="input_organism_selector" type="select" label="Select organism"> + <option value="Human" selected="true">Homo sapiens</option> + <option value="Mouse">Mus musculus</option> + <option value="Zebrafish">Zebrafish (Danio rerio)</option> + <option value="XTropicalis">X.Tropicalis</option> + <option value="Bacteria/MycoTube">M. tuberculosis</option> + </param> + <when value="Human"> + <param name="version" type="select" label="Select genome vesion"> + <option value="hg19" selected="true">hg19</option> + <option value="hg18">hg18</option> + </param> + </when> + <when value="Mouse"> + <param name="version" type="select" label="Select genome vesion"> + <option value="mm8" >mm8</option> + <option value="mm9" selected="true">mm9</option> + <option value="mm10" >mm10</option> + </param> + </when> + <when value="Zebrafish"> + <param name="version" type="select" label="Select genome vesion"> + <option value="zv9" selected="true">zv9</option> + </param> + </when> + <when value="XTropicalis"> + <param name="version" type="select" label="Select genome vesion"> + <option value="xenTro2" >xenTro2</option> + <option value="xenTro3" selected="true">xenTro3</option> + </param> + </when> + <when value="Bacteria/MycoTube"> + <param name="version" type="select" label="Select genome vesion"> + <option value="H37Rv" selected="true">H37Rv</option> + </param> + </when> +</conditional> + +<conditional name="use_reg"> + <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/> + </when> + </conditional> + + <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/> + </inputs> + <outputs> + <data name="outputPNG" format="png" label="Peaks Stats (png)"> + <filter>(if_PDF == 0)</filter> + </data> + <data name="outputPDF" format="pdf" label="Peaks Stats (pdf)"> + <filter>(if_PDF == True)</filter> + </data> + + <data name="stats" format="tabular" label="Annotated Peaks (ChIP)"/> + <data name="log" format="log" label=".LOG for Annotated Peaks"/> + <data name="statsControl" format="tabular" label="Annotated Peaks (Control)"> + <filter>(use_control['use_control_selector'] == 'yes')</filter> + </data> + </outputs> + <tests> + <test> + <param name="inputfile" value="peaks_test.bed"/> + <param name="minScore" value="0.0"/> + <param name="use_control_selector" value="yes"/> + <param name="controlfile" value="peaks_control.bed"/> + <param name="left" value="-2000"/> + <param name="right" value="2000"/> + <param name="EnhLeft" value="-30000"/> + <param name="DownGene" value="5000"/> + <param name="input_organism_selector" value="Mouse"/> + <param name="version" value="mm9"/> + <param name="use_reg_selector" value="yes"/> + <param name="regfile" value="Probesets_FC1.5_10022011.txt"/> + <param name="if_PDF" value="1"/> + <output name="outputPDF" file="test_annotatePeaks_1.dat" ftype="pdf"/> + <output name="stats" file="test_annotatePeaks_2.dat" ftype="tabular"/> + <output name="log" file="test_annotatePeaks_3.dat" ftype="log"/> + <output name="statsControl" file="test_annotatePeaks_4.dat" ftype="tabular"/> + </test> + </tests> + <help> +**What it does** + +This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution + + </help> + <citations> + <citation type="bibtex">@article{Boeva01102012, + author = {Boeva, Valentina and Lermine, Alban and Barette, Camille and Guillouf, Christel and Barillot, Emmanuel}, + title = {Nebula—a web-server for advanced ChIP-seq data analysis}, + volume = {28}, + number = {19}, + pages = {2517-2519}, + year = {2012}, + doi = {10.1093/bioinformatics/bts463}, + URL = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.abstract}, + eprint = {http://bioinformatics.oxfordjournals.org/content/28/19/2517.full.pdf+html}, + journal = {Bioinformatics} + }</citation> + </citations> +</tool>