--- a/macros.xml	Fri Jun 10 09:58:03 2016 -0400
+++ b/macros.xml	Fri Jan 13 14:15:42 2017 -0500
@@ -4,13 +4,18 @@
             <exit_code range="1:" level="fatal" description="Job Failed" />
             <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
+            <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
     </xml>
     <token name="@GENERAL_PARAMETERS@">
             -frag_tol "${fragment_tol}"
+            ### -frag_ppm
             -prec_tol "${precursor_ion_tol}"
             -prec_ppm "${precursor_ion_tol_units}"
+            ### -digestion
+            ### multiple enzymes?
             -enzyme "${enzyme}"
+            ### -specificity
             #set $fixed_mods_str = $fixed_modifications or ''
             #set $variable_mods_str = $variable_modifications or ''
             #if $fixed_mods_str
@@ -21,12 +26,13 @@
             #end if
             -min_charge $min_charge
             -max_charge $max_charge
+            ### value per enzyme
             -mc $missed_cleavages
             -fi $forward_ion
             -ri $reverse_ion
     </token>
-    <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
-    <token name="@SEARCHGUI_VERSION@">2.9</token>
+    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
+    <token name="@SEARCHGUI_VERSION@">3.1.4</token>
     <xml name="general_options">
         <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
             help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">