Changes to liftOver tool: Modified the liftOver.loc file and changed the script files as required.

tools/extract/liftOver_wrapper.py

@@ -17,28 +17,17 @@ infile = sys.argv[1]
 outfile1 = sys.argv[2]
 outfile2 = sys.argv[3]
 in_dbkey = sys.argv[4]
-out_dbkey = sys.argv[5]
+mapfilepath = sys.argv[5]
 
-#ensure dbkeys are set
+#ensure dbkey is set
 if in_dbkey == "?": 
     stop_err( "Input dataset genome build unspecified, click the pencil icon in hte history item to specify it." )
-if out_dbkey == "?": 
-    stop_err( "No build selected for conversion." )
 
-#Check if the Mapping file exists    
-#example file path: hg18ToHg17.over.chain
-mapfilename = in_dbkey + "To" + out_dbkey.capitalize()  + ".over.chain"
-# TODO: Ticket # 167 - These hard-coded paths need to be removed
-mapfilepath = "/depot/data2/galaxy/" + in_dbkey + "/liftOver/" + mapfilename
 cmd_line = "liftOver " + infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null 2>&1"
 
 if not os.path.isfile( mapfilepath ):
-    stop_err( "Mapping information from %s to %s is not currently available."  % ( in_dbkey, out_dbkey ) )
+    stop_err( "%s mapping is not currently available."  % ( mapfilepath.split('/')[-1].split('.')[0] ) )
 try:
     os.system( cmd_line )
 except Exception, exc:
-    stop_err( "Exception caught attempting conversion: %s"  % str( exc ) )
-
-print "%s converted to %s" % ( in_dbkey, out_dbkey )
-  
-    
+    stop_err( "Exception caught attempting conversion: %s"  % str( exc ) )

tools/extract/liftOver_wrapper.xml

@@ -6,7 +6,7 @@
       <validator type="unspecified_build" />
     </param>
     <param name="to_dbkey" type="select" label="To">
-      <options from_file="/depot/data2/galaxy/liftOver.loc" name_col="1" value_col="1">
+      <options from_file="/depot/data2/galaxy/liftOver.loc" name_col="1" value_col="2">
         <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0"/>
       </options>
     </param> 
@@ -19,7 +19,7 @@
   <tests>
     <test>
       <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
-      <param name="to_dbkey" value="panTro2" />
+      <param name="to_dbkey" value="/depot/data2/galaxy/hg18/liftOver/hg18ToPanTro2.over.chain" />
       <output name="out_file1" file="5_liftover_mapped.bed"/>
       <output name="out_file2" file="5_liftover_unmapped.bed"/>
     </test>

tools/extract/liftOver_wrapper_code.py

@@ -1,6 +1,9 @@
 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'])
+    #Assuming the path of the form liftOverDirectory/hg18ToHg17.over.chain (This is how the mapping chain files from UCSC look.)
+    to_dbkey = param_dict['to_dbkey'].split('.')[0].split('To')[1]
+    to_dbkey = to_dbkey[0].lower()+to_dbkey[1:]
+    out_data['out_file1'].set_dbkey(to_dbkey)
+    out_data['out_file2'].set_dbkey(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 ]"