view masscomb_dbsearch_converter.xml @ 13:c91d0d09cb0c default tip

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<tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.5">
	<description> Convert search results to MzIdentML (aka mzid) format</description>
	<requirements>
		<requirement type="set_environment">PWIZ_3_0_5622_PATH</requirement>
		<requirement type="package" version="3.05622">proteowizard</requirement>
	</requirements>
	<!-- 
	   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 
	   -outputMsMsFragmentationData $outputMsMsFragmentationData
	   -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>
		    		<option value="proteomediscoverer_pepxml">Proteome Discoverer (pepxml) [beta]</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>
	      	<when value="proteomediscoverer_pepxml">
	      		<param name="inputFile" type="data" format="any" label="MS/MS search results (pepxml)"/>
	      	</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>
	  <param name="outputMsMsFragmentationData" type="boolean" checked="false" 
	  label="Output MS/MS fragmentation data" 
	  help="NB: this will add to the output also the fragment ions related to each peptide identification. 
	  NB2: Fragment ion annotation data is 
		inferred based on new calculations triggered by this conversion tool. 
		This is done because fragment ion annotation information is not present 
		in X!Tandem file (X!Tandem SLEDGEHAMMER (2013.09.01) and previous)"/>
     	
	</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, OMSSA or Proteome Discoverer peptide identification results to mzIdentML format.
It uses the library at http://code.google.com/p/mzidentml-parsers/ 
-----


  </help>
</tool>