Mercurial > repos > xuebing > bed_closest

changeset 0:ae1369ab462a

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Uploaded
author xuebing
date Sat, 31 Mar 2012 13:49:46 -0400
parents
children 434ca790f5a1
files bed_closest.xml
diffstat 1 files changed, 32 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_closest.xml	Sat Mar 31 13:49:46 2012 -0400
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+<tool id="bed_closest" name="bed_closest">
+  <description>find closest intervals</description>
+  <command>bed_closest -a $inputa -b $inputb $strandness -d $no -t $tie> $output_data
+  </command>
+  <inputs>
+      <param name="inputa" type="data" format="interval,bam,bed,gff,vcf" label="Input A (-a)"/>
+      <param name="inputb" type="data" format="interval,bam,bed,gff,vcf" label="Input B (-b)"/>          
+      <param name="strandness" type="select" label="Strand requirement" >
+		<option value="" selected="true"> none </option>
+        <option value="-s" > -s: closest feature on the same strand</option>
+        <option value="-S" > -S: closest feature on the opposite strand </option>
+      </param>
+      
+    <param name="no" label="Only look for non-overlaping features" type="boolean" truevalue="-no" falsevalue="" checked="False"/>
+              <param name="tie" type="select" label="Strand requirement" >
+		<option value="all" selected="true"> report all ties </option>
+        <option value="first" > report the first that occurred</option>
+        <option value="last" > report the last that occurred </option>
+      </param>
+        </inputs>
+  <outputs>
+    <data format="input" name="output_data"/> 
+  </outputs>
+  <help>
+
+**What it does**
+
+This is a wrapper for closestBed.
+
+  </help>
+</tool>
+