view ccat_int2bed.xml @ 3:313e20192e7e draft default tip

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<tool id="ccat_int2bed" name="CCAT2bed" version="1.0">
  <description>Convert CCAT output (intervals) into Bed</description>
  <requirements>
  	<container type="docker">institutcuriengsintegration/ccattobed:1.0</container>
  </requirements>
  <command interpreter="bash">
ccat2bed.sh -f $inputfile -t $minHeight -o $output -g $genome_selector -n $name -r ${__root_dir__}
 </command>
   <inputs>
    <param name="name" type="text" label="type of experiment" value="track_name"/>
    <param name="inputfile" type="data" label="CCAT output interval file" value="CCAT output interval file" format="interval"/>          
    <param name="genome_selector" type="select" label="Select the genome under study">
        <option value="hg19" selected="true">hg19</option>	
        <option value="hg18">hg18</option>
        <option value="mm9">mm9</option>   
        <option value="mm10">mm10</option>    
    </param>
    <param name="minHeight" type="integer" label="Minimal read count per peak to consider" value="0"/>

  </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 CCAT

  </help>
</tool>