--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msclust2.0.1.xml	Thu Jan 16 13:10:00 2014 +0100
@@ -0,0 +1,289 @@
+<tool name="MsClust" id="msclust2" version="2.0.1">
+	<description>Extracts fragmentation spectra from aligned data</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 
+	                    //////////////////////////
+	       
+	       TODO in command below: add conditionals according to options of using or NOT the tolerances/thresholds from previous steps 
+	    -->
+	<command interpreter="java -jar ">
+	    MsClust.jar 
+	   	-peaksFileName $inputPeaks 
+	   	-dataType $dataType
+        -imputationMethod $imputationMethod.type
+        #if $imputationMethod.type == "valueRange"
+        	-rangeUpperLimit $imputationMethod.rangeUpperLimit
+        #end if
+		-plInputFormat "metalign" 
+		-potDensFuncType $potDensFuncType.type 
+		-centerSelectionType $centerSelectionType.type 
+		-clusteringType $clusteringType.type 
+		-neighborhoodWindowSize $potDensFuncType.pdf_neighborhoodWindowSize 
+		-clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion
+		-pearsonDistTreshold $potDensFuncType.pdf_pears_treshold
+		-pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf
+		-pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold
+		-pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope
+		-scanDistTol $potDensFuncType.pdf_scan_toler 
+		-scanDistanceConfidence $potDensFuncType.pdf_scan_conf  
+		-centrotypesOut $centrotypesOut 
+		-simOut $simOut
+		-micOut $micOut
+		-mspOut $mspOut 
+		-classOut $classOut
+		-outReport $htmlReportFile
+	    -outReportPicturesPath $htmlReportFile.files_path
+        #if $clusteringType.type == "fuzzyCMeans"
+        	-fcmMembershipWeightingExponent $clusteringType.fcmMembershipWeightingExponent 
+			-fcmStopCriterion $clusteringType.fcmStopCriterion
+			-fcmCorrelationWeight $clusteringType.fcmCorrelationWeight
+			-fcmFinalAssemblyType $clusteringType.finalClusterAssembly.type
+			#if $clusteringType.finalClusterAssembly.type == "membershipBased"
+				-fcmMembershipCutoff $clusteringType.finalClusterAssembly.fcmMembershipCutoff
+			#end if
+        #end if
+		-verbose "false"
+	    #if $advancedSettings.settings == True
+	    	-advancedSettings YES
+	    	-saturationLimit $advancedSettings.saturationLimit
+	    	-sampleSelectionSortType $advancedSettings.sampleSelectionSortType
+	    	-simSelectionAlgorithm $advancedSettings.simSelectionAlgorithm
+	    	-simMassFilter "$advancedSettings.simMassFilter"
+	    	-simMembershipThreshold $advancedSettings.simMembershipThreshold
+	    	-simSaturationThreshold $advancedSettings.simSaturationThreshold
+	    	-simAbsenseThreshold $advancedSettings.simAbsenseThreshold
+	    	-micMembershipThreshold $advancedSettings.micMembershipThreshold
+	    	-peakIntensityCorrectionAlgorithm $advancedSettings.peakIntensityCorrectionAlgorithm
+        #else
+        	-advancedSettings YES
+        	-sampleSelectionSortType SIM_INTENSITY
+        	-peakIntensityCorrectionAlgorithm CORRELATION_BASED
+        #end if
+	    
+	</command>
+	<inputs>
+	<!--  <param name="rankingWeightConfig" type="text" area="true" size="11x70" label="NB - TEST VERSION" 
+value="VERSION BEING TESTED AT THIS MOMENT...NOT READY FOR USE..."/>
+	-->
+	 	<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />
+		<param name="dataType" type="select" size="30" label="Data type">
+				<option value="gcms"  selected="true">GC-MS</option>
+				<option value="lcms">LC-MS</option>
+			</param>
+	 	<conditional name="imputationMethod">
+			<param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps">
+				<option value="none" >none</option>
+				<option value="metot" selected="true">MeTot</option>
+				<option value="valueRange">Values range</option>
+			</param>
+			<when value="valueRange">
+				<param name="rangeUpperLimit" type="integer" size="10" value="0" label="Range upper limit" help="values up to this limit will be considered 'generated' values"  />
+			</when>
+		</conditional>		    
+	 	<conditional name="potDensFuncType">
+		    <param name="type" type="select" size="30" label="Select PD function type =====================================================">
+		      <option value="original" selected="true">Original</option>
+		    </param>
+		    <when value="original">
+		      <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks"  />
+		      <param name="pdf_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
+		      <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
+		      <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
+		      <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
+		    </when>
+		</conditional>
+		<conditional name="centerSelectionType">
+		    <param name="type" type="select" label="Initial Centers selection type ==================================================" >
+		      <option value="original" selected="true">Original - Subtractive potential reductions with stop criterion and REUSE tolerances (from PD function)</option>
+		    </param>
+		    <when value="original">
+		      <param name="cs_pears_pd_reductionTreshold" type="float" size="10" value="0.8" label="Potential Density reduction (0.0 - 1.0)"  />
+		      <param name="cs_pears_pd_reductionSlope" type="float" size="10" value="0.01" label="Potential Density reduction softness "  />
+		      <param name="cs_stop_criterion" type="float" size="10" value="2" label="Stop Criterion "  />
+			</when>
+		</conditional>
+		<conditional name="clusteringType">
+		    <param name="type" type="select" label="Classify using ===========================================================">
+		      <option value="original" selected="true">Original - Fuzzy clustering, keep original centers and REUSE (scan distance) tolerances</option>
+		      <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option>
+		    </param>
+		    <when value="original">
+		    <!-- nothing -->
+			</when>
+		    <when value="originalNewTol">
+		      <param name="clust_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans"  />
+		      <param name="clust_scan_slope" type="float" size="10" value="2" label="Peak Width margin softness"  />
+		    </when>
+		    <when value="fuzzyCMeans">
+				<param name="fcmMembershipWeightingExponent" type="float" size="10" value="2.0" label="Membership Weighting Exponent" help="Influences cluster center repositioning in the iterations 1.1 (exploratory) to around 3.0 (conservative)" />
+				<param name="fcmStopCriterion" type="float" size="10" value="0.05" label="Stop Criterion" help="When convergence is 'reached' (e.g. 0.05 means memberships only changed with 5% in last iteration)" />
+				<param name="fcmCorrelationWeight" type="float" size="10" value="2" label="Correlation weight factor" help="Increase this if you think the correlation is reliable (e.g. you have a high number of samples)" />
+				<conditional name="finalClusterAssembly">
+					<param name="type" type="select" label="Final cluster assembly" >
+				      <option value="original" selected="true">Original - distance based</option>
+				      <option value="membershipBased">Membership based</option>
+				    </param>
+					<when value="membershipBased">
+						<param name="fcmMembershipCutoff" type="select" label="Maximum allowed peak overlap" >
+							<option value="0.05" >~7 clusters</option>
+							<option value="0.10" >~5 clusters</option>
+							<option value="0.20" >~3 clusters</option>
+						</param>
+					</when>
+					<when value="original">
+					    <!-- nothing -->
+					</when>
+				</conditional>
+		    </when>
+		</conditional>
+		
+		<param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time (in some cases up to a few extra minutes)"/>
+     	
+        <conditional name="advancedSettings">
+     		<param name="settings" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Advanced settings ========================================================"/>
+     		<when value="Yes">
+     			<param name="saturationLimit" optional="true" type="integer" size="10" label="Saturation limit (optional)" help="fill in if you have saturation problems in your data"  />
+	 			<param name="sampleSelectionSortType"  type="select" label="Sample selection scheme for spectrum peak intensity correction algorithm (optional/experimental)" help="The intensity values to use to select the samples for each cluster/metabolite in which it is most intense/abundant. These samples are used in the peak intensity correction (see parameter below). Use this option to try to avoid samples that have insufficient signal or saturation."  >
+     				<option value="None">None</option>
+     				<!-- in order of best FORWARD scoring when tested on /test/data/report_test_sets/(P2) Relative peak heights in spectra/Input (Test set 1) -->
+     				<option value="SIM_INTENSITY" selected="true">SIM intensities</option>
+		    		<option value="MAX_INTENSITY">Maximum intensities</option>
+     				<option value="CENTROTYPE_INTENSITY">Centrotype peak intensities</option>
+		    		<option value="MIC_INTENSITY">MIC intensities</option>		    		
+     			</param>
+     			<param name="peakIntensityCorrectionAlgorithm"  type="select" label="Spectrum peak intensity correction algorithm (optional/experimental)" help="Whether spectrum peak heights should be adjusted according to their membership to the cluster or to their correlation to the cluster's centrotype ion"  >
+     				<option value="MEMBERSHIP_BASED">Membership based (msclust 1.0 mode)</option>
+		    		<option value="CORRELATION_BASED" selected="true">Correlation based</option>
+     			</param>     			
+     			<param name="simSelectionAlgorithm" type="select" label="SIM selection algorithm (experimental)" help="Set this if you want to deviate from the standard which is: allow shared SIM peaks for GC-MS data, and force unique SIM peaks for LC-MS data">
+     				<option value="" selected="true"></option>
+     				<option value="uniqueSIM">Unique SIM peak</option>
+		    		<option value="sharedSIM">Shared SIM peak</option>
+     			</param>
+     			<param name="simMassFilter" type="text" optional="true" size="30" label="SIM mass exclusion list" help="Comma-separated list of masses NOT to use as SIM peaks. E.g. '73,147,...' " />
+     			<param name="simMembershipThreshold" optional="true" type="float" size="10" label="SIM membership threshold" help="Minimum membership a peak should have to qualify as a SIM candidate. E.g. 0.8 " />
+     			<param name="simSaturationThreshold" optional="true" type="float" size="10" label="SIM saturation threshold (%)" help="Maximum % of samples in which a SIM candidate peak may be saturated. If the candidate peak exceeds this threshold, then another peak is chosen. If no peak can be found this criteria, mass 0 is reported" />
+     			<param name="simAbsenseThreshold" optional="true" type="float" size="10" label="SIM absence threshold (%)" help="Maximum % of samples in which a SIM candidate peak may be absent. If the candidate peak exceeds this threshold, then another peak is chosen. If no peak can be found meeting this criteria, mass 0 is reported" />
+     			
+     			<param name="micMembershipThreshold" optional="true" type="float" size="10" label="MIC membership threshold" help="Minimum membership a peak should have to be counted in the MIC sum. E.g. 0.8 " />
+     			
+     		</when>
+     	</conditional>	
+
+     	
+	</inputs>
+	<outputs>
+	  <data name="centrotypesOut" format="msclust.csv" label="${tool.name} on ${on_string} - centrotypes file"/>
+	  <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/>
+	  <data name="micOut" format="msclust.csv" label="${tool.name} on ${on_string} - MIC file"/>
+	   <data name="mspOut" format="msp" label="${tool.name} on ${on_string} - SPECTRA file"/>
+	  <data name="classOut" format="msclust.csv" label="${tool.name} on ${on_string} - Classification file"/>
+	  <data name="htmlReportFile" format="html" label="${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 -->
+	</tests>
+  <help>
+
+<!-- see also http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html#hyperlink-targets -->
+  
+.. class:: infomark
+  
+This tool extracts spectra from ion-wise aligned MS(/MS) results. It uses expression profiles and 
+retention times of the putative ions to cluster them. Each cluster is then used to generate 
+one spectrum containing the clustered ions (peaks). 
+
+.. image:: $PATH_TO_IMAGES/msclust_summary.png 
+
+
+-----
+
+**Output**
+
+This tools returns a number of ouptut files and a small report. 
+
+**Parameters index**
+
+
+*Select the approach used for imputing missing values:* only select this if you have used a specific method to 
+fill in the data gaps in the input file. One example is replacing zero values by some randomly generated low value.
+If MeTot is chosen, then a value is considered generated if: the value contains a dot '.' and some number 
+other than 0 (zero) after the dot. 
+
+*Effective Peaks:* Neighborhood window size to consider when calculating density. Smaller values increase 
+performance but are less reliable.
+
+*Peak Width, in scans:* Scan window width of scans to consider 'close'. One can see this as the 
+'tolerated variation in scans' for the apex positions of the fragment peaks composing a cluster. 
+Note: if MetAlign was used, this is the variation *after* pre-processing by MetAlign.   
+
+*Peak Width confidence:* The higher the confidence, the stricter the threshold.
+
+*Correlation threshold (0.0 - 1.0):* Tolerance center for pearson distance calculation. The higher this value, 
+the higher the correlation between 2 items has to be for them to be considered 'close'. 
+
+*Correlation threshold confidence:* The higher the confidence, the stricter the threshold. `More...`__
+
+*Potential Density reduction (0.0 - 1.0):* Reduction tolerance center for pearson distance calculation. 
+The higher this value, the less the low correlated items get reduced, getting a chance to form a cluster of their own. 
+
+*Potential Density reduction softness:* Reduction curve slope for pearson distance tolerance. Lower 
+values = stricter separation at the value determined in 'Potential Density reduction' above  
+(TODO review this comment). 
+
+*Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations 
+
+.. __: javascript:window.open('$PATH_TO_IMAGES/confidence_and_slope_params_explain.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
+
+
+-----
+
+**Output files described below**
+
+-----
+
+*SPECTRA:* this file can be submitted to NIST for identification of the spectra.
+
+`Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_  
+
+.. _Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation: javascript:window.open('$PATH_TO_IMAGES/sample_sel_and_peak_height_correction.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
+
+-----
+
+*MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count 
+values (corrected by their membership) for all MEASURED cluster ions in the given sample.
+
+The MIC for a **cluster i** in **sample s**, where **cluster i** has **n** members is thus: 
+
+sum ( [intensity of member n in **sample s**] x [membership value of member n in **cluster i** ] )
+
+-----
+
+*SIM:* stands for Selective Ion Mode ->  it contains, for each cluster, the intensity values of the 
+most representative member ion peak of this cluster. The most representative member peak is the one with the 
+highest membership*average_intensity. This definition leads to conflicts as a peak can have a 
+membership in two or more clusters. The assignment of a SIM peak to a cluster depends on 
+the configured data type (LC or GC-MS). NB: this can be overruled in the "advanced settings":
+
+(1) LC-MS SIM: select SIM peak only once and for the centrotype in which this specific mass has its 
+highest membership; for neighboring centrotypes use its "second best SIM", etcetera. In other words,
+if the SIM peak has been identified as the SIM in more than 1 cluster, assign as SIM to the cluster 
+with highest membership. Continue searching for other SIM peaks to assign to the other clusters until 
+all ambiguities are solved.
+
+(2) GC-MS SIM: the SIM peak can be "shared" by multiple clusters. However, the intensity values are corrected
+by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not 
+"shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file. 
+
+`Click here for more details on the SIM output file`_  
+
+.. _Click here for more details on the SIM output file: javascript:window.open('$PATH_TO_IMAGES/sample_SIM.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
+
+
+
+  </help>
+</tool>