--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_dbsearch_converter.xml	Wed Jan 08 11:34:51 2014 +0100
@@ -0,0 +1,82 @@
+<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>