# HG changeset patch
# User sjung
# Date 1495600524 14400
# Node ID 0ea254c514b7494e488a4b7f3f76ce5c0c76b413
# Parent  29760e9a840b0751fb626b17fa40492b29939eb2
Uploaded

diff -r 29760e9a840b -r 0ea254c514b7 fseq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fseq.xml	Wed May 24 00:35:24 2017 -0400
@@ -0,0 +1,45 @@
+<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>