From f27ef3634f4c2bfa527f2047184d466fcecc29d5 Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Sun, 8 Jun 2008 19:28:45 +0000
Subject: [PATCH] Changing liftOver input from BED to Interval in order to
 preserve the contents of columns other than the chromosome, start and end
 columns. This information was previously being lost during Interval to BED
 conversion.

---
 tools/extract/liftOver_wrapper.xml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index 3e5c91d7746..d6c542f8bf2 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -2,7 +2,7 @@
   <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 format="interval" name="input" type="data" label="Convert coordinates of">
       <validator type="unspecified_build" />
     </param>
     <param name="to_dbkey" type="select" label="To">
@@ -15,8 +15,8 @@
     </param> 
   </inputs>
   <outputs>
-    <data format="bed" name="out_file1" />
-    <data format="bed" name="out_file2" />
+    <data format="input" name="out_file1" />
+    <data format="input" name="out_file2" />
   </outputs>
   <requirements>
     <requirement type="binary">liftOver</requirement>
@@ -41,6 +41,10 @@ Make sure that the genome build of the input dataset is specified (click the pen
 
 The **To** list will be empty if we don't carry any liftover mappings corresponding to the genome build of the input dataset. 
 
+.. class:: warningmark
+
+This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case, it will return empty output datasets.
+
 -----
 
 .. class:: infomark