--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mascot_to_pepxml.xml	Mon Mar 04 16:28:18 2013 -0500
@@ -0,0 +1,31 @@
+<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.0">
+	<requirements>
+	    <requirement type="package" version="1.1.9">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-1.1.9 do mascot_to_pepxml.rb $input_file -o $output -d $database</command>
+<inputs>
+
+	<param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
+	<param name="database" type="select" format="text" >
+	    <label>Database</label>
+		<options from_file="pepxml_databases.loc">
+			<column name="name" index="0" />
+			<column name="value" index="2" />
+		</options>
+	</param>
+	
+
+</inputs>
+<outputs>
+	<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
+</outputs>
+
+<help>
+	Convert mascot results from mascotdat to pepXML
+</help>
+
+</tool>