diff ExtendBedRegions.xml @ 0:cb1c17dddc14 default tip

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ExtendBedRegions.xml	Wed Mar 25 13:32:42 2015 -0600
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+
+<tool id="extend_bed_regions_1" name="Expand or contract regions">
+  <description>in a BED file by a fixed number of bases</description>
+  <version_string>echo 1.0.0</version_string>
+  <command interpreter="perl">extend_bed_regions $in_bed $extent $strand $out_bed</command>
+  <inputs>
+    <param format="bed" name="in_bed" type="data" label="BED file whose regions should be modified"/>
+    <param name="extent" type="integer" value="50" label="Number of bases to extend each BED region (negative values cause contraction)"/>
+    <param name="strand" type="select" display="radio" label="Which end to extend?" help="If the BED file contains strand info, extension will be strand specific. Otherwise, the positive strand is assumed">
+      <option value="5">5'</option>
+      <option value="3">3'</option>
+      <option value="both" selected="true">Both</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_bed" format="bed" type="data" label="BED file with extended/contracted regions"/>
+  </outputs>
+
+  <tests/>
+
+  <help>
+This tool expands each regions defined in a BED file by the specified amount, at the specified end(s). If expanded regions overlap, they are merged.
+ </help>
+
+</tool>