<tool id="fseq" name="FSeq" version="F-Seq: 1.85">
  <description>A Feature Density Estimator for High-Throughput Sequence Tags</description>
  <requirements>
    <requirement type="package">java</requirement>
    <requirement type="package">fseq</requirement>
  </requirements>
  <command>
<![CDATA[
fseq -f $fragSize -l $featLen -of $outputFormat -s $wiggleTrackStep -t $threshold 
#for $i, $j in enumerate($fd):
    $j.input
#end for  
; cat *.bed >  $output 
]]>
  </command>

  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>

  <inputs>
    <repeat name="fd" title="bed format inputs" min="1">
      <param help="" label="input" name="input" type="data"/>
    </repeat>
     <param name="fragSize" type="integer" value="0" label="Fragment Size" />    
     <param name="featLen" type="integer" value="600" label="feature length" />
     <param name="outputFormat" type="select" label="output format" >
        <option value="wig">Wiggle</option>
        <option value="bed">Bed</option>
        <option value="npf">narrowPeak</option>
     </param>
     <param name="wiggleTrackStep" type="integer" value="1" label="wiggle track step" />
     <param name="threshold" type="float" value="4.0" label="threshold" />
   </inputs>

   <outputs>
         <data format="bed,wig" label="${tool.name} on ${on_string}" name="output" />
   </outputs>
   <tests>
     <test>
     </test>
   </tests>
   <help>
   </help>
</tool>