--- a/segemehl.xml	Wed Feb 04 06:52:06 2015 -0500
+++ b/segemehl.xml	Thu Feb 05 08:25:13 2015 -0500
@@ -10,7 +10,7 @@
         #if $refGenomeSource.genomeSource == "history":
             segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome;
         #else:
-            #set $temp_index = ${refGenomeSource.index.fields.index_path}
+            #set $temp_index = $refGenomeSource.index.fields.index_path
         #end if
 
 
@@ -52,10 +52,10 @@
         -A $accuracy
         -H $hitstrategy
         #if str( $prime5 ).strip():
-            -P $prime5
+            -P "$prime5"
         #end if
         #if str( $prime3 ).strip():
-            -Q $prime3
+            -Q "$prime3"
         #end if
         $polyA
         $autoclip