<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1">
    <description>Converts a ProtXML file to a table</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
    </requirements>
    <command>
        protxml_to_table.rb
          $invert_probs
        $input_file
        -o $output
    </command>
    <inputs>
        <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
        <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" />
    </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_pproph_protproph.prot.xml" format="protxml"/>
          <output name="output" format="tabular">
              <assert_contents>
                  <has_text text="AVQKYLTAHEQSK" />
              </assert_contents>
          </output>
      </test>
    </tests>
    <help>
**What it does**

Converts a ProtXML file to a tab separated table 

    </help>
</tool>