<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.0">
	<requirements><requirement type="package">protkgem</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>rvm 1.9.3@protk-1.1.9 do pepxml_to_table.rb $input_file -o $output</command>


<inputs>

	<param name="input_file" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>

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

<help>
	Convert a pepXML file to Tab delimited text
</help>

</tool>