--- a/omssa.xml	Thu Jun 06 01:33:45 2013 -0400
+++ b/omssa.xml	Thu Jun 06 15:37:22 2013 +1000
@@ -1,7 +1,7 @@
 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1">
 
    <requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
     	<requirement type="package" version="2.1.9">omssa</requirement>
     	<requirement type="package" version="2.2.27">blast</requirement>
    </requirements>
@@ -9,9 +9,12 @@
 
 	<description>Run an OMSSA MS/MS Search</description>
 		
-	<command>#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.fasta_file
+	<command>rvm 1.9.3@protk-1.2.2 do omssa_search.rb
+
+		#if $database.source_select=="built_in":
+		-d $database.dbkey 
+		#else
+		-d $database.fasta_file
 		#end if
 		
 		--var-mods='
@@ -26,7 +29,28 @@
 		$searched_ions
 		'
 		
-		$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --num-peaks-for-multi-isotope-search $multi_isotope $use_average_mass $respect_precursor_charges --max-hit-expect $max_hit_expect --intensity-cut-off $intensity_cut_off
+		$input_file 
+		-o $output 
+		-r 
+
+		--enzyme=$enzyme 
+
+		--precursor-ion-tol-units=$precursor_tolu 
+
+		-v $missed_cleavages 
+
+		-f $fragment_ion_tol 
+
+		-p $precursor_ion_tol 
+
+		--num-peaks-for-multi-isotope-search $multi_isotope 
+
+		$use_average_mass 
+		$respect_precursor_charges 
+
+		--max-hit-expect $max_hit_expect 
+
+		--intensity-cut-off $intensity_cut_off
 
 	</command>