--- a/mascot_to_pepxml.xml	Tue Mar 05 00:18:41 2013 -0500
+++ b/mascot_to_pepxml.xml	Sun Jun 09 08:17:38 2013 -0500
@@ -1,29 +1,80 @@
 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" 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="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
   <description>Converts a mascot results file to pepXML</description>
 
-<command>rvm 1.9.3@protk-1.2.0 do mascot_to_pepxml.rb $input_file -o $output -d $database</command>
+<command>rvm 1.9.3@protk-1.2.2 do mascot_to_pepxml.rb 
+	$input_file 
+
+	-o $output 
+
+	#if $database.source_select=="built_in":
+	-d $database.dbkey
+	#else 
+	-d $database.fasta_file
+	#end if
+
+	#if $explicit_enzyme.explicit_enzyme_use
+	--enzyme $explicit_enzyme.enzyme
+	#end if
+
+	$shortid
+
+</command>
 <inputs>
 
+
 	<param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
-	<param name="database" type="select" format="text" >
-	    <label>Database</label>
-		<options from_file="pepxml_databases.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>
-	
+
+	<conditional name="database">
+		<param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
+			<option value="built_in">Built-In</option>
+			<option value="input_ref">Uploaded fasta file</option>
+		</param>
+		<when value="built_in">
+			<param name="dbkey" type="select" format="text" >
+				<label>Database</label>
+				<options from_file="pepxml_databases.loc">
+					<column name="name" index="0" />
+					<column name="value" index="2" />
+				</options>
+			</param>
+		</when>
+		<when value="input_ref">
+			<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+		</when>
+	</conditional>
+
+	<param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
+
+	<conditional name="explicit_enzyme">
+		<param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
+		<when value="false" />
+		<when value="true">
+			<param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
+		</when>
+	</conditional>
+
+
 
 </inputs>
 <outputs>
 	<data format="raw_pepxml" metadata_source="input_file" name="output" label="${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="F002832.dat"/>
+      		<output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> 
+    	</test>
+    	
+  	</tests>
+
 <help>
 	Convert mascot results from mascotdat to pepXML
 </help>