# HG changeset patch
# User nikos
# Date 1405423122 14400
# Node ID 37da191c7760c15e0aa3e498082f7a4378fb616b
# Parent  dfe85aeb51bbf0d2a757a9e149b6cf2d1802e5da
Uploaded

diff -r dfe85aeb51bb -r 37da191c7760 bedClip.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedClip.xml	Tue Jul 15 07:18:42 2014 -0400
@@ -0,0 +1,53 @@
+<tool id="bedClip" name="bedClip">
+  <description> Remove lines from bed file that refer to off-chromosome places.</description>
+  <command interpreter="bash"> 
+	## Set genome assembly 
+
+	#set $Genome = str( $genome_cond.genome )
+	#if str( $genome_cond ) == 'OTHER':
+		#set $Genome = str( $genome_cond.genome_other )
+	#end if
+	
+	bedClip.sh $input $Genome $output
+  </command>
+  <inputs>
+    <param name="input" type="data" format="bed" label="Input"/>
+    <conditional name="genome_cond">
+      <param name="genome" type="select" label="Genome Assembly">
+        <option value="hg19">Human (Homo sapiens): hg19</option>
+        <option value="hg18">Human (Homo sapiens): hg18</option>
+        <option value="mm10">Mouse (Mus musculus): mm10</option>
+        <option value="mm9">Mouse (Mus musculus): mm9</option>
+        <option value="ce10">C. elegans: ce10</option>
+        <option value="ce6">C. elegans: ce6</option>
+        <option value="dm3">D. melanogaster: dm3</option>
+        <option value="OTHER">Other</option>
+      </param>
+      <when value="OTHER">
+        <param name="genome_other" type="text" label="Other genome assemly"/>
+      </when>
+      <when value="hg19" type="text" />
+      <when value="hg18" type="text" />
+      <when value="mm10" type="text" />
+      <when value="mm9" type="text" />
+      <when value="ce10" type="text" />
+      <when value="ce6" type="text" />
+      <when value="dm3" type="text" />
+    </conditional>
+
+  </inputs>
+  
+  <outputs>
+    <data format="input" name="output"/> 
+  </outputs>
+  <help>
+**What it does**
+bedClip - Remove lines from bed file that refer to off-chromosome places.
+
+**Usage**
+
+  bedClip input.bed chrom.sizes output.bed
+
+  </help>
+</tool>
+