<tool id="protxml_to_table_1" name="ProtXML 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 ProtXML file to a table</description>

	<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>