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

@@ -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