<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>