--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sedmat.xml	Wed Jan 08 11:39:16 2014 +0100
@@ -0,0 +1,144 @@
+<tool name="SedMat" id="sedmat1" version="1.0.2">
+	<description>Matches MS and MS/MS results</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 ">
+	    SedMat_cli.jar 
+	    -pl $inputMS 
+	    -plInputFormat apml 
+	    -ppids $fileType.inputFormatType.ppidsFile 
+	    -ppidsFileGrouping $fileType.type 
+	    -ppidsInputFormat $fileType.inputFormatType.ppidsInputFormat
+	    -ppidsFileDescription $fileType.inputFormatType.ppidsFile.name  
+	    #if $fileType.inputFormatType.ppidsInputFormat == "mzid"
+			-spectraDataFile $fileType.inputFormatType.spectraDataFile
+		#end if 
+	    -out $outputData 
+	    -outUnmatchedMS2 $outUnmatchedMS2
+	    -mtol $mtol 
+	    -rttol $rttol 
+	    -rtShiftDetectionWindow $rtShiftDetectionWindow
+	    -matchOnSameSourceOnly $matchOnSameSourceOnly
+	    -chargeStatesToGenerate $chargeStatesToGenerate
+	    -outReport $htmlReportFile
+	    -outReportPicturesPath $htmlReportFile.files_path
+        #if $troubleshoot1.troubleshootPeakLocations == True
+        	-troubleshootPeakLocations YES
+        	-mStart $troubleshoot1.mStart
+        	-mEnd $troubleshoot1.mEnd
+        	-rtStart $troubleshoot1.rtStart
+        	-rtEnd $troubleshoot1.rtEnd
+        	-filterSourceName $troubleshoot1.filterSourceName
+        #end if
+        #if $matchOnNamingConvention.match == True
+        	-matchOnNamingConvention YES
+        	-namingConventionCodesForMatching $matchOnNamingConvention.namingConventionCodesForMatching
+        #end if
+        	    
+	</command>
+	
+	<inputs>
+	 	
+  		<param name="inputMS" type="data" format="apml" label="MS data (APML format)" />
+	 	<!-- possible option <validator type="metadata" check="base_name" message="Metadata missing, click the pencil icon in the history item and set base_name."/> -->
+
+	 	<conditional name="fileType">
+		    <param name="type" type="select" label="Peptide identification file grouping type">
+		      <option value="single" selected="true">single-File</option>
+		      <option value="fileSet">fileSet</option>
+		    </param>
+		    <when value="single">
+		      <conditional name="inputFormatType">
+		      	<param name="ppidsInputFormat" type="select" label="MS/MS input format">
+			    	<option value="mzid" selected="true">mzIdentML on mzML</option>
+			    	<option value="apml">APML</option>
+				</param>
+				<when value="mzid">
+		      		<param name="spectraDataFile" type="data" format="mzml" label="MS/MS spectra file (mzml)"/>
+		      		<param name="ppidsFile" type="data" format="mzid" label="MS/MS peptide identifications file (mzidentml)"/>
+		      	</when>
+		      	<when value="apml">
+		      		<param name="ppidsFile" type="data" format="apml" label="MS/MS peptide identifications file (apml)">
+		      			<!-- TODO - find out how to use
+		      			<validator type="expression" message="You already selected this file as the MS data file.">value.id == inputMS,{"inputMS":$inputMS},{}</validator>-->
+		      		</param>
+		      	</when>
+		      </conditional>
+		    </when>
+		    <when value="fileSet">
+		      <conditional name="inputFormatType">
+		      	<param name="ppidsInputFormat" type="select" label="inputFormat">
+			    	<option value="mzid" selected="true">mzIdentML on mzML</option>
+				</param>
+				<when value="mzid">
+		      		<param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/>
+		      		<param name="ppidsFile" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/>
+		      	</when>
+		      </conditional>
+		    </when>
+		</conditional>
+		<param name="mtol" type="integer" size="10" value="50" 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"/>
+
+		<param name="matchOnSameSourceOnly" type="boolean" checked="false" label="Match peaks from same source only" help="If you want this, you might have to inform how to match the source files"/>
+     	<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.'"/>
+     		</when>
+     	</conditional>	 
+
+ 		<param name="chargeStatesToGenerate" type="select" display="checkboxes" multiple="true" label="Generate extra charge states" help="The selected charge states will be generated for each MS2 feature ">
+	      	<option value="1" selected="true">1</option>
+	      	<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>
+		</param>
+
+   		<param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time"/>
+     	
+     	<conditional name="troubleshoot1">
+     		<param name="troubleshootPeakLocations" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Troubleshoot ms1/ms2 peak locations" help="Small trial run to check if the MS and MS/MS peak lists in their current states can easily be matched "/>
+     		<when value="Yes">
+     			<param name="mStart" optional="false" type="integer" size="10" value="100" label="Set m/z start " />
+     			<param name="mEnd" optional="false" type="integer" size="10" value="1000" label="Set m/z end " />
+				<param name="rtStart" optional="false" type="integer" size="10" value="10" label="Set rention time start (minutes) " />
+				<param name="rtEnd" optional="false" type="integer" size="10" value="20" label="Set rention time end (minutes) " />
+				<param name="filterSourceName" type="text" size="100" value="" label="Restrict matching to a specific subset of the files " help="Part of a file name that occurs in both a ms1 and ms2 file (e.g. 'RibO_1_msE1')"/>
+     		</when>
+     	</conditional>
+     	
+	</inputs>
+	<outputs>
+	  <data name="outputData" format="apml" label="${inputMS.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="inputMS"></data>
+	  <data name="outUnmatchedMS2" format="csv" label="${inputMS.metadata.base_name} - ${tool.name} on ${on_string}: unmatched MS2 features CSV" metadata_source="inputMS"></data>
+	  <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report">
+	 	<!-- If the expression is false, the file is not created -->
+	  	<filter>( summaryReport == True )</filter>
+	  </data>
+	</outputs>
+	<tests>
+	  <!--  find out how to use -->
+	  <test>
+	  </test>
+	</tests>
+  <help>
+  
+.. class:: infomark
+  
+This tool matches MS and MS/MS results. SEDMAT stands for "Single Experiment Data Matching Tool".
+It can match peaks found in the MS spectra with the peptides found using the MS/MS spectra.
+The result is the list of MS peaks annotated with peptides and proteins.
+
+-----
+
+**Output example**
+
+This tools returns APML output, a Cytoscape network (.xgmml) of the matches and Retention Time plots (.pdf). 
+
+  </help>
+</tool>