<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0">
	<requirements>
         <container type="docker">iracooke/protk-1.4.1</container>
	    <requirement type="package" version="1.4">protk</requirement>
	    <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>

	<description>Converts a tandem result file to pepXML</description>

	<command>
		tandem_to_pepxml.rb $input_file -o $output 
	</command>

	<inputs>
		<param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
	</inputs>

	<outputs>
		<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
	</outputs>

	<help>
		Convert X!Tandem results to pepXML
	</help>

	<tests>
		<!-- Just test that the tool runs and produces vaguely correct output -->
		<test>
		    <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
		    <output name="output" format="raw_pepxml">
		        <assert_contents>
					<has_text text="SQVFQLESTFDV" />
		        </assert_contents>
		    </output>
		</test>
	</tests>

</tool>