# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1397488293 -7200
# Node ID 40ec8770780de51552858042ff704e3ef381a662
# Parent  d56c18ed0f77eec821b64f20b60e837473f955e4
* Added support for pepxml (and more specifically for
  ProteomeDiscoverer 1.4). Tested with ProteomeDiscoverer 1.4 pepxml.
* Improved HTML report of NapQ tool.
* Fixed issue that was preventing SEDMAT matching from running
  in parallel/multi-threaded.

diff -r d56c18ed0f77 -r 40ec8770780d Csv2Apml.jar
Binary file Csv2Apml.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d MsFilt.jar
Binary file MsFilt.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d NapQ.jar
Binary file NapQ.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d PRIMS.jar
Binary file PRIMS.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d ProgenesisConv.jar
Binary file ProgenesisConv.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d Quantifere.jar
Binary file Quantifere.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d Quantiline.jar
Binary file Quantiline.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d README.rst
--- a/README.rst	Fri Mar 28 14:43:46 2014 +0100
+++ b/README.rst	Mon Apr 14 17:11:33 2014 +0200
@@ -20,6 +20,11 @@
 ============== ======================================================================
 Date            Changes
 -------------- ----------------------------------------------------------------------
+April  2014    * Added support for pepxml (and more specifically for 
+                 ProteomeDiscoverer 1.4). Tested with ProteomeDiscoverer 1.4 pepxml. 
+               * Improved HTML report of NapQ tool.
+               * Fixed issue that was preventing SEDMAT matching from running  
+                 in parallel/multi-threaded.  
 January 2014   * first release via Tool Shed
 November 2013  * multiple tools used internally at PRI 
 end 2011       * first tool
diff -r d56c18ed0f77 -r 40ec8770780d SedMat_cli.jar
Binary file SedMat_cli.jar has changed
diff -r d56c18ed0f77 -r 40ec8770780d csv2apml.xml
--- a/csv2apml.xml	Fri Mar 28 14:43:46 2014 +0100
+++ b/csv2apml.xml	Mon Apr 14 17:11:33 2014 +0200
@@ -22,7 +22,7 @@
 		       label="Column name for precursor m/z" />     			
 
 		<param name="rt" type="text" optional="false" size="30" 
-		       label="Column name for precursor rt" />
+		       label="Column name for precursor rt  (nb: rt in minutes)" />
      	
 		<param name="charge" type="text" optional="false" size="30" 
 		       label="Column name for precursor charge (z)" />
diff -r d56c18ed0f77 -r 40ec8770780d msfilt.xml
--- a/msfilt.xml	Fri Mar 28 14:43:46 2014 +0100
+++ b/msfilt.xml	Mon Apr 14 17:11:33 2014 +0200
@@ -1,4 +1,4 @@
-<tool name="MsFilt" id="msfilt" version="1.0.3">
+<tool name="MsFilt" id="msfilt" version="1.0.4">
 	<description>Filters annotations based MS/MS peptide identification and annotation quality measures</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -27,6 +27,10 @@
 	    -addRawIntensityInfo $addRawIntensityInfo
     	-outReport $htmlReportFile
 	    -outReportPicturesPath $htmlReportFile.files_path
+	    #if $containsPepxml.pepxmlInSet == True
+        	-pepxmlDataType $containsPepxml.pepxmlDataType
+			-pepxmlGeneratedBy $containsPepxml.pepxmlGeneratedBy
+        #end if
 	</command>
 	
 	<inputs>
@@ -37,9 +41,35 @@
    		               SEDMAT or Quantiline tools." />
    		
    		<repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified.">
-   			<param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" />
+   			<param name="identificationsFile" type="data" format="apml,pepxml,mzidentml,prims.fileset.zip" label="Identifications file (APML, pepxml, MZIDENTML or MZIDENTML fileSet)" />
    		</repeat>
    		
+   		<!-- ================== PEPXML specific ================== -->
+   		<conditional name="containsPepxml">
+	  		<param name="pepxmlInSet" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 
+	    		label="Identifications set contains one or more files in pepxml format"
+	    		help="Indicate whether one or more (Optional) Peptide identification files is in pepxml format. Support for pepxml is still considered 'beta'."/> 
+   			<when value="Yes">
+	      		<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>
+	      	<when value="No">
+     		</when>
+     	</conditional>
+   		<!-- ================== END - PEPXML specific ================== -->
+   		
      	<!-- 
      	<param name="maxNrRankings" type="integer" size="10" value="0" label="Maximum nr. of items to leave in the final ranking (set=0 for no limit) " />
      	-->
@@ -62,13 +92,16 @@
 &#xd;&#xa;qmBCOS =&gt; best correlation with other sibling peptide (correl),1
 "/>
 
-		<param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration" 
+		<param name="statisticalMeasuresConfig" type="text" area="true" size="8x70" label="Statistical measures configuration" 
 		help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). 
 		The format is: SM alias => SM name,type,mode[min/max]. "
 value="smXTD =&gt; MS:1001330,XSLASH!Tandem:expect,min
 &#xd;&#xa;pvCSVEX =&gt; p_value,CSV_EXPORT,min
 &#xd;&#xa;smAUTO_LIKELIHOOD =&gt; AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max
 &#xd;&#xa;smLIKELIHOOD =&gt; LOGLIKELIHOOD,PLGS/Databank-search,max
+&#xd;&#xa;smPercoProb =&gt; Percolator: probability,Percolator probability,max
+&#xd;&#xa;smPercoPEP =&gt; Percolator: PEP,Percolator PEP,min
+&#xd;&#xa;smPercoQval =&gt; Percolator: q-Value,Percolator q-Value,max
 "/>
 
      	<param name="filterOutUnannotatedAlignments" type="boolean" checked="true" 
@@ -117,7 +150,9 @@
 		#for $i, $s in enumerate( $annotationSourceFiles )
 			${s.identificationsFile}
 			## also print out the datatype in the next line, based on previously configured datatype
-			#if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__):
+			#if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('pepxml').__class__):
+				pepxml
+			#elif isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__):
 				apml
 			#else:
         		mzid
diff -r d56c18ed0f77 -r 40ec8770780d napq.xml
--- a/napq.xml	Fri Mar 28 14:43:46 2014 +0100
+++ b/napq.xml	Mon Apr 14 17:11:33 2014 +0200
@@ -1,4 +1,4 @@
-<tool name="NapQ" id="napq" version="0.0.1">
+<tool name="NapQ" id="napq" version="0.0.3">
 	<description>'no alignment' (alignment-free) peptide quantification</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
diff -r d56c18ed0f77 -r 40ec8770780d quantifere.xml
--- a/quantifere.xml	Fri Mar 28 14:43:46 2014 +0100
+++ b/quantifere.xml	Mon Apr 14 17:11:33 2014 +0200
@@ -1,4 +1,4 @@
-<tool name="Quantifere" id="quantifere1" version="1.0.2">
+<tool name="Quantifere" id="quantifere1" version="1.0.3">
 	<description>Protein Inference by Peptide Quantification patterns</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -61,7 +61,7 @@
      		</when>
      	</conditional>
    		
-   		<param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration" 
+   		<param name="statisticalMeasuresConfig" type="text" area="true" size="8x70" label="Statistical measures configuration" 
 				help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). 
 				The format is: SM alias => SM name,type,mode[min/max]. Leaving this configuration out while these are present in the
 				dataset will have the effect that they will be wrongly used as a regular scoring scheme, having effect on for example
@@ -70,6 +70,9 @@
 &#xd;&#xa;pvCSVEX =&gt; p_value,CSV_EXPORT,min
 &#xd;&#xa;smAUTO_LIKELIHOOD =&gt; AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max
 &#xd;&#xa;smLIKELIHOOD =&gt; LOGLIKELIHOOD,PLGS/Databank-search,max
+&#xd;&#xa;smPercoProb =&gt; Percolator: probability,Percolator probability,max
+&#xd;&#xa;smPercoPEP =&gt; Percolator: PEP,Percolator PEP,min
+&#xd;&#xa;smPercoQval =&gt; Percolator: q-Value,Percolator q-Value,max
 "/>
 <!-- keep value attribute above aligned like this to avoid white spaces in the value -->				
    		<param name="quantificationDataToUse" type="select" 
diff -r d56c18ed0f77 -r 40ec8770780d sedmat.xml
--- 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"/>