<tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1">
	<description> Convert search results to MzIdentML (aka mzid) format</description>
	<!-- 
	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
	       java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 
	                    //////////////////////////
	    -->
	<command interpreter="java -jar">
	   MassComb.jar 
	   -action DBSEARCHCONVERT 
	   -fileGrouping $fileType.type 
	   -searchResultsFormat $fileType.inputFormatType.inputFormat
	    #if $fileType.inputFormatType.inputFormat == "xtandem"
	    	-isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero
        #end if
	   -inputFile $fileType.inputFormatType.inputFile 
	   -outputFile $outputFile 
	</command>
	<inputs>
		<conditional name="fileType">
	    <param name="type" type="select" label="select file grouping type">
	      <option value="single" selected="true">single-File</option>
	      <option value="fileSet">fileSet</option>
	    </param>
	    <when value="single">
	      <conditional name="inputFormatType">
	      	<param name="inputFormat" type="select" label="inputFormat">
		    		<option value="xtandem">X!Tandem</option>
		    		<option value="omssa">OMSSA</option>
			</param>
			<when value="xtandem">
	      		<param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/>
	      		<param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. ">
			      <option value="true" selected="true">Yes, starting at 0</option>
			      <option value="false">No, starting at 1</option>
			    </param>
	      	</when>
	      	<when value="omssa">
	      		<param name="inputFile" type="data" format="omx" label="MS/MS search results"/>
	      	</when>
	      </conditional>
	    </when>
	    <when value="fileSet">
	    	<conditional name="inputFormatType">
		    	<param name="inputFormat" type="select" label="inputFormat">
			    		<option value="xtandem">X!Tandem</option>
			    		<option value="omssa">OMSSA</option>
				</param>
				<when value="xtandem">
	      			<param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results" />
	      			<param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. ">
				      <option value="true" selected="true">Yes, starting at 0</option>
				      <option value="false">No, starting at 1</option>
				    </param>
		      	</when>
		      	<when value="omssa">
		      		<param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/>
		      	</when>
		      </conditional>
	    </when>
	  </conditional>
	</inputs>
	<outputs>
	  <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} ">
		<change_format>
		    <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/>
		</change_format>
		</data>
	</outputs>
	<tests>
	</tests>
  <help>
  
.. class:: infomark
  
This tool translates X!Tandem and OMSSA results to mzIdentML format.
It uses the library at http://code.google.com/p/mzidentml-parsers/ 
-----


  </help>
</tool>