--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AddNamesToBED.xml	Wed Mar 25 13:09:20 2015 -0600
@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+
+<tool id="add_names_to_bed_1" name="Add names to a BED file">
+  <description>based on overlap with a named regions BED file</description>
+  <version_string>echo 1.0.0</version_string>
+  <command interpreter="perl">add_names_to_bed $in_unnamed_bed $in_named_bed $out_renamed_bed $out_log</command>
+  <inputs>
+    <param format="bed" name="in_unnamed_bed" type="data" label="BED file to rename" help="BED file without useful names for each region reported"/>
+    <param format="bed" name="in_named_bed" type="data" label="BED file with names to inherit" help="BED file with useful names for each region (4th column)"/>
+  </inputs>
+  <outputs>
+    <data name="out_renamed_bed" format="bed" type="data" label="BED file with renamed regions"/>
+    <data name="out_log" format="text" type="data" label="Renaming stats"/>
+  </outputs>
+
+  <tests/>
+
+  <help>
+This tool replaces names (4th column) in a BED file, based on overlap of those regions with named regions 
+provided in another BED file.  For example, a list of exome dud regions could be annotated with the gene
+names in the dud regions, by running this tool with the UCSC refFlat BED file as the named regions source.
+ </help>
+
+</tool>