Mercurial > repos > jbrayet > annotategenes_histones_1_0_docker
changeset 1:0d3b8e48c423 draft
Uploaded
author | jbrayet |
---|---|
date | Tue, 05 Jan 2016 08:05:52 -0500 |
parents | 9947321ac2a0 |
children | cfede5ba1e76 |
files | annotateGenes_hist_wrapper.xml |
diffstat | 1 files changed, 146 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotateGenes_hist_wrapper.xml Tue Jan 05 08:05:52 2016 -0500 @@ -0,0 +1,146 @@ +<!--annotateGenes - 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="annotateGenes_histones" name="Annotation of genes with ChIP-seq peaks (histones)" version="1.0"> + <description>Caclulates statistics for TSS and gene body</description> + <requirements> + <container type="docker">institutcuriengsintegration/annotategeneshistones:1.0</container> + </requirements> + <command interpreter="bash"> +#if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotateGenes_hist_wrapper.sh -f $inputfile -y $log -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" # annotateGenes_hist_wrapper.sh -f $inputfile -y $log -c $controlfile -b $use_control.bootstraps -x $statsControl -o $outputPNG -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" # annotateGenes_hist_wrapper.sh -y $log -f $inputfile -e $regfile -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" # annotateGenes_hist_wrapper.sh -f $inputfile -c $controlfile -b $use_control.bootstraps -x $statsControl -l $left -y $log -o $outputPNG -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" #annotateGenes_hist_wrapper.sh -f $inputfile -y $log -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" # annotateGenes_hist_wrapper.sh -f $inputfile -y $log -c $controlfile -b $use_control.bootstraps -x $statsControl -o $outputPDF -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" # annotateGenes_hist_wrapper.sh -y $log -f $inputfile -e $regfile -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" # annotateGenes_hist_wrapper.sh -f $inputfile -c $controlfile -b $use_control.bootstraps -x $statsControl -l $left -y $log -o $outputPDF -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"/> + <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"/> + <param name="bootstraps" type="select" label="Number of bootstrap iterations" help="Using bootstrap resampling from the control will significantly slow down the procedure"> + <option value="1" selected="true" >do not use bootstrap resampling</option> + <option value="10" >10</option> + <option value="100" >100</option> + </param> + </when> + </conditional> + + <param name="left" type="integer" label="Define Promoter is a region up to X bp upstream gene TSS" value="-1000"/> + <param name="right" type="integer" label="Define Immediate Downstream is a region up to X bp downstream gene TSS" value="1000"/> + <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="Rat">Rattus norvegicus</option> + <option value="Cow">Cow</option> + <option value="Zebrafish">Zebrafish (Danio rerio)</option> + <option value="XTropicalis">X.Tropicalis</option> + <option value="Bacteria/MycoTube">M. tuberculosis</option> + <option value="Celegans">C. elegans</option> + <option value="Drosophila">D. melanogaster</option> + </param> + <when value="Human"> + <param name="version" type="select" label="Select genome vesion"> + <option value="hg38">hg38</option> + <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="Rat"> + <param name="version" type="select" label="Select genome vesion"> + <option value="rn5">rn5</option> + </param> + </when> + <when value="Cow"> + <param name="version" type="select" label="Select genome vesion"> + <option value="bosTau7">bosTau7</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> + <when value="Celegans"> + <param name="version" type="select" label="Select genome vesion"> + <option value="ce10" selected="true">ce10</option> + </param> + </when> + <when value="Drosophila"> + <param name="version" type="select" label="Select genome vesion"> + <option value="dm6" selected="true">dm6</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="Gene Stats (png)"> + <filter>(if_PDF == 0)</filter> + </data> + <data name="outputPDF" format="pdf" label="Gene Stats (pdf)"> + <filter>(if_PDF == True)</filter> + </data> + + <data name="stats" format="tabular" label="Annotated Genes (ChIP)"/> + <data name="log" format="tabular" label=".LOG for Annotated Genes"/> + <data name="statsControl" format="tabular" label="Annotated Genes (Control)"> + <filter>(use_control['use_control_selector'] == 'yes')</filter> + </data> + </outputs> + <help> +**What it does** + +This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution + + </help> +</tool>