<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.1">
    <description>Converts a tandem result file to pepXML</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Failure" />
    </stdio>
    <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>
    <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>
    <help>
        Convert X!Tandem results to pepXML
    </help>
</tool>