<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0">

	<requirements>
            <container type="docker">iracooke/protk-1.4.1</container>
	    <requirement type="package" version="1.4">protk</requirement>
   </requirements>



  <description>Converts a pepXML file to a tab delimited text file</description>


<!-- 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="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
</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>