view [APliBio]Nebula tools suite/Nebula/MakeStatsCHiPSeq/makeStatsChIPSeq_wrapper.xml @ 3:1c699789d6d3 draft

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<tool id="makeStatsChIPSeq" name="MakeStatsChIPSeq" version="1.0">
  <description>Get peak height distribution</description>
  <command interpreter="bash">
#if str( $ifPDF ) == 'Yes' #makeStatsChIPSeq_wrapper.sh -f $inputfile -c $controlfile -m $minHeight -o $outputPDF -s $maxHeight -u $stats -p 1 #else #  makeStatsChIPSeq_wrapper.sh -f $inputfile -c $controlfile -m $minHeight -o $outputPNG -s $maxHeight -u $stats -p 0 #end if
 </command>
   <inputs>
   
    <param name="inputfile" type="data" label="ChIP: File with peaks" value="ChIP-Seq File" format="txt"/>
    <param name="controlfile" type="data" label="Control: File with peaks" value="Control File" format="txt"/>
    <param name="minHeight" type="integer" label="Minimal peak height to consider" value="3"/>
    <param name="maxHeight" type="integer" label="Maximal peak height to consider" value="50"/>

    <param name="ifPDF" type="select" label="Do you want to have a PDF image (default PNG)?">
        <option value="No" selected="true">No</option>
        <option value="Yes">Yes</option>
    </param>
  </inputs>
  <outputs>

    <data name="stats" format="tabular" label="Peak height distribution (stats)"/>   

    <data name="outputPNG" format="png" label="Peak height distribution (png)">
    <filter>(ifPDF == "No")</filter>
    </data>
    <data name="outputPDF" format="pdf" label="Peak height distribution (pdf)">
    <filter>(ifPDF == "Yes")</filter>
    </data>

  </outputs>
  <help>
**What it does**

This tool creates a .png (or .pdf) file with distribution of peaks heights for ChIP and Control sample

  </help>
</tool>