<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1">
    <description>Converts a pepXML file to a tab delimited text file</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
    </requirements>
    <!-- Note .. the input file is assumed to be the first argument -->
    <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command>
    <inputs>
        <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
        <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" metadata_source="input_file" label="${input_file.display_name}.tsv" />
    </outputs>
    <tests>
        <!-- Just test that the tool runs and produces vaguely correct output -->
        <test>
            <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/>
            <output name="output" format="csv">
                <assert_contents>
                    <has_text text="ANTNNYAPKSSR" />
                </assert_contents>
            </output>
        </test>
    </tests>
<help>
    Convert a pepXML file to Tab delimited text
</help>
</tool>