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<!--annotateGenes - developed by Jocelyn Brayet <[e-mail]>
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" name="Annotation of genes with ChIP-seq peaks (transcription factors)" version="1.0">
  <description>Caclulates statistics for promoters, enhancers, introns/exons, etc.</description>
  <requirements>
    <container type="docker">institutcuriengsintegration/annotategenes: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_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_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_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_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_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_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_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_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="-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="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>