--- a/tandem.xml	Sun Jan 06 19:12:02 2013 -0500
+++ b/tandem.xml	Mon Mar 04 01:51:22 2013 -0500
@@ -1,11 +1,16 @@
 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0">
-	<requirements><requirement type="package">protkgem</requirement></requirements>
+
+   <requirements>
+    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
+    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
+   </requirements>
+
 	<description>Run an X!Tandem Search</description>
 
 	<command>
 		#if $database.source_select=="built_in":
-		tandem_search.rb -d $database.dbkey 
-		#else #tandem_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey 
+		#else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
 		#end if
 
 		--var-mods='
@@ -24,8 +29,6 @@
 
 		$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
 		
-		
-		
 	</command>
 
 	<inputs>	
@@ -110,6 +113,18 @@
 		<data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
 	</outputs>
 
+	<tests>
+    	<test>
+    		<param name="source_select" value="input_ref"/>
+	      	<param name="fasta_file" value="bsa.fasta"/>
+   		   	<param name="input_file" value="bsa.mzML"/>
+      		<param name="variable_mods" value="15.994915@M"/>
+      		<param name="fixed_mods" value="57.021464@C"/>
+      		<param name="allow_multi_isotope_search" value="false"/>
+      		<output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> 
+    	</test>
+  	</tests>
+
 
   <help>