--- a/sedmat.xml	Fri Mar 28 14:43:46 2014 +0100
+++ b/sedmat.xml	Mon Apr 14 17:11:33 2014 +0200
@@ -1,4 +1,4 @@
-<tool name="SedMat" id="sedmat1" version="1.0.2">
+<tool name="SedMat" id="sedmat1" version="1.0.3">
 	<description>Matches MS and MS/MS results</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -12,10 +12,14 @@
 	    -ppidsFileGrouping $fileType.type 
 	    -ppidsInputFormat $fileType.inputFormatType.ppidsInputFormat
 	    -ppidsFileDescription "$fileType.inputFormatType.ppidsFile.name"  
-	    #if $fileType.inputFormatType.ppidsInputFormat == "mzid"
+	    #if $fileType.inputFormatType.ppidsInputFormat == "MZML_MZIDENTML_COMBI"
 			-spectraDataFile $fileType.inputFormatType.spectraDataFile
-		#end if 
-	    -out $outputData 
+		#end if
+		#if $fileType.inputFormatType.ppidsInputFormat == "pepxml"
+			-pepxmlDataType $fileType.inputFormatType.pepxmlDataType
+			-pepxmlGeneratedBy $fileType.inputFormatType.pepxmlGeneratedBy
+		#end if
+		-out $outputData 
 	    -outUnmatchedMS2 $outUnmatchedMS2
 	    -mtol $mtol 
 	    -rttol $rttol 
@@ -52,10 +56,11 @@
 		    <when value="single">
 		      <conditional name="inputFormatType">
 		      	<param name="ppidsInputFormat" type="select" label="MS/MS input format">
-			    	<option value="mzid" selected="true">mzIdentML on mzML</option>
+			    	<option value="MZML_MZIDENTML_COMBI" selected="true">mzIdentML on mzML</option>
 			    	<option value="apml">APML</option>
+			    	<option value="pepxml">pepxml (beta support)</option>
 				</param>
-				<when value="mzid">
+				<when value="MZML_MZIDENTML_COMBI">
 		      		<param name="spectraDataFile" type="data" format="mzml" label="MS/MS spectra file (mzml)"/>
 		      		<param name="ppidsFile" type="data" format="mzid" label="MS/MS peptide identifications file (mzidentml)"/>
 		      	</when>
@@ -65,6 +70,25 @@
 		      			<validator type="expression" message="You already selected this file as the MS data file.">value.id == inputMS,{"inputMS":$inputMS},{}</validator>-->
 		      		</param>
 		      	</when>
+		      	<when value="pepxml">
+		      		<param name="ppidsFile" type="data" format="pepxml" label="MS/MS peptide identifications file (pepxml)"/>
+		      		<param name="pepxmlDataType" type="select" label=">> Type of data stored in the pepxml"
+		      		       help="Options marked with (*) are ProteomeDiscoverer specific scenarios">
+				    	<option value="" selected="true">--Please select--</option>
+			    		<option value="single_2d" >2D LC-MS runs, one per msms_run_summary</option>
+				    	<option value="multi_2d">(*) 2D LC-MS runs, multiple runs (e.g. rx.F1 to rx.FN) merged as a 'single' msms_run_summary</option>
+				    	<option value="single_1d">1D LC-MS runs, one per msms_run_summary</option>
+					</param>
+					<param name="pepxmlGeneratedBy" type="select" label=">> pepxml generated by"
+						help="Some tools, like ProteomeDiscoverer 1.4, have specific issues in their pepxml generation logic. Correctly indicating the tool used here will ensure known issues are taken 
+						     into consideration when the file is parsed." >
+						<option value="" selected="true">--Please select--</option>
+			    		<option value="proteome_discoverer_v1.4">ProteomeDiscoverer 1.4</option>
+				    	<option value="other">Other</option> 
+					</param>
+					
+		      	</when>
+		      	
 		      </conditional>
 		    </when>
 		    <when value="fileSet">
@@ -79,7 +103,7 @@
 		      </conditional>
 		    </when>
 		</conditional>
-		<param name="mtol" type="integer" size="10" value="50" label="m/z tolerance (ppm) " />
+		<param name="mtol" type="float" size="10" value="50.0" label="m/z tolerance (ppm) " />
 		<param name="rttol" type="integer" size="10" value="150" label="Rention time tolerance (seconds) " />
 		<param name="rtShiftDetectionWindow" type="integer" size="10" value="20" label="Rention time shift detection window (seconds) " help="Size of the window to use for average rt shift calculations"/>
 
@@ -87,7 +111,7 @@
      	<conditional name="matchOnNamingConvention">
      		<param name="match" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Match using naming convention" help="Use a list of codes that occur in the file names and that link them together."/>
      		<when value="Yes">
-     			<param name="namingConventionCodesForMatching" type="text" size="100" value="" label="List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,etc.'"/>
+     			<param name="namingConventionCodesForMatching" type="text" size="100" value="" label=">> List of codes in naming convention" help="Add the CSV list of codes that occur in the file names and that link them together. E.g. '_F1,_F2,_F3,_F4,_F5,_F6,_F7,etc.'"/>
      		</when>
      		<when value="No">
      		</when>
@@ -98,7 +122,9 @@
 	      	<option value="2" selected="true">2</option>
 	      	<option value="3" selected="true">3</option>
 	      	<option value="4" selected="true">4</option>
-	      	<option value="5">5</option>
+	      	<option value="5" selected="true">5</option>
+	      	<option value="6" >6</option>
+	      	<option value="7" >7</option>
 		</param>
 
    		<param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time"/>