diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 912c755c015..75163d8c41d 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -27,6 +27,9 @@
     <tool file="encode/gencode_partition.xml" />
     <tool file="encode/random_intervals.xml" />
   </section>
+  <section name="LiftOver" id="liftOver">
+    <tool file="extract/liftOver_wrapper.xml" />
+  </section>
   <section name="Text Manipulation" id="textutil">
     <tool file="filters/fixedValueColumn.xml" />
     <tool file="stats/column_maker.xml" />
diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver_wrapper.py
new file mode 100644
index 00000000000..d072101bd21
--- /dev/null
+++ b/tools/extract/liftOver_wrapper.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python2.4
+#Guru
+"""
+Converts coordinates from one build/assembly to another using liftOver binary and mapping files downloaded from UCSC.
+"""
+
+import sys, os, string
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+    
+if len(sys.argv) != 6:
+    stop_error("USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey")
+
+infile = sys.argv[1]
+outfile1 = sys.argv[2]
+outfile2 = sys.argv[3]
+in_dbkey = sys.argv[4]
+out_dbkey = sys.argv[5]
+
+#ensure dbkeys are set
+if in_dbkey == "?": 
+    stop_err("You must specify a build to the input dataset in order to covert genome coordinates.")
+if out_dbkey == "?": 
+    stop_err("Please specify a build for the output dataset using the 'To' dropdown menu.")
+
+#Check if the apping file exists    
+#example file path: hg18ToHg17.over.chain
+mapfilename = in_dbkey + "To" + out_dbkey[0].capitalize() + out_dbkey[1:] + ".over.chain"
+mapfilepath = "/depot/data2/galaxy/" + in_dbkey + "/liftOver/" + mapfilename
+try:
+    open(mapfilepath, 'r')
+except Exception, ex:
+    stop_err("Mapping information from %s to %s is unavailable." %(in_dbkey, out_dbkey))
+    
+print "Mapping from %s to %s" %(in_dbkey,out_dbkey)
+try:
+    cmd_line = "liftOver " + infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null 2>&1"
+    os.system(cmd_line)
+except Exception, exc:
+    print >>sys.stderr, exc
+  
+    
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
new file mode 100644
index 00000000000..bc7d4b49470
--- /dev/null
+++ b/tools/extract/liftOver_wrapper.xml
@@ -0,0 +1,52 @@
+<tool id="liftOver1" name="Convert genome coordinates">
+  <description> between assemblies and genomes</description>
+  <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command>
+  <inputs>
+    <param format="bed" name="input" type="data" label="Convert coordinates of"/>
+    <param name="to_dbkey" type="genomebuild" label="To" />
+  </inputs>
+  <outputs>
+    <data format="bed" name="out_file1" />
+    <data format="bed" name="out_file2" />
+  </outputs>
+  <!--
+  <tests>
+    <test>
+      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
+      <param name="to_dbkey" value="panTro2" />
+      <output name="out_file1" file="5_liftover_mapped.bed"/>
+      <output name="out_file2" file="5_liftover_unmapped.bed"/>
+    </test>
+  </tests>
+  -->
+  <help>
+
+.. class:: warningmark
+
+Make sure that the genome build is specified for the input dataset (click the pencil icon if it is not specified).
+
+-----
+
+**What it does**
+
+This tool converts genome coordinates and annotation files between assemblies and genomes. It outputs 2 files, one containing all the mapped coordinates and one containing the unmapped coordinates (if any). 
+
+-----
+
+**Example**
+
+Running this tool to convert the following hg16 intervals into hg18 intervals::
+
+    chrX  85170   112199  AK002185  0  +
+    chrX  110458  112199  AK097346  0  +
+    chrX  112203  121212  AK074528  0  -
+
+will return the following hg18 intervals::
+
+    chrX  132991  160020  AK002185  0  +
+    chrX  158279  160020  AK097346  0  +
+    chrX  160024  169033  AK074528  0  -
+
+</help>
+<code file="liftOver_wrapper_code.py"/>
+</tool>
diff --git a/tools/extract/liftOver_wrapper_code.py b/tools/extract/liftOver_wrapper_code.py
new file mode 100644
index 00000000000..0d7ec90629a
--- /dev/null
+++ b/tools/extract/liftOver_wrapper_code.py
@@ -0,0 +1,6 @@
+def exec_before_job(app, inp_data, out_data, param_dict, tool):
+    out_data['out_file1'].set_dbkey(param_dict['to_dbkey'])
+    out_data['out_file2'].set_dbkey(param_dict['to_dbkey'])
+    out_data['out_file1'].name = out_data['out_file1'].name + " [ MAPPED COORDINATES ]"
+    out_data['out_file2'].name = out_data['out_file2'].name + " [ UNMAPPED COORDINATES ]"
+