annotate [APliBio]Nebula tools suite/Nebula/Peak2Bed/peak2bed.xml @ 3:1c699789d6d3 draft

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<tool id="peak2bed" name="PeaksToBed" version="1.0">
  <description>Convert FindPeaks output (.peaks) into Bed</description>
  <command interpreter="perl">peak2bed.pl -f $inputfile -t $minHeight -o $output -g ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${inputfile.dbkey}.len -n $name</command>
   <inputs>
    <param name="name" type="text" label="type of experiment" value="track name"/>
    <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="txt"/>          

    <param name="minHeight" type="integer" label="Minimal peak height to consider" value="3"/>
  </inputs>
  <outputs>
    <data name="output" format="bed" label="${name}.bed"/>   
  </outputs>
  <help>
**What it does**

This tool creates a .bed file using .peaks output of FindPeaks

  </help>
</tool>