--- a/msgfplus_search.xml	Sat Jun 14 17:49:14 2014 -0400
+++ b/msgfplus_search.xml	Wed Jun 25 19:00:11 2014 -0400
@@ -46,8 +46,8 @@
         --min-pep-charge=$min_pep_charge
         --num-reported-matches=$num_reported_matches
         --java-mem=$java_mem
-        #unless $pepxml_output_use:
-        --no-pepxml
+        #if $pepxml_output_use:
+        --pepxml
         #end unless
     </command>
 
@@ -103,7 +103,7 @@
         <param name="enzyme" type="select" format="text">
             <label>Enzyme</label>
             <option value="0">unspecific cleavage</option>
-            <option value="1">Trypsin</option>
+            <option value="1" selected="true">Trypsin</option>
             <option value="2">Chymotrypsin</option>
             <option value="3">Lys-C</option>
             <option value="4">Lys-N</option>