# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1389958768 -3600
# Node ID 2c1c9f0d8aa6735604786e7dd03e23792a213951
# Parent a35b55bfe96ca0c6a1f047a20d4d8f4ee43763df
using normal versioning
diff -r a35b55bfe96c -r 2c1c9f0d8aa6 msclust.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/msclust.xml Fri Jan 17 12:39:28 2014 +0100
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+
+ Extracts fragmentation spectra from aligned data
+
+
+ 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
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+ ( summaryReport == True )
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+
+.. 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')
+
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diff -r a35b55bfe96c -r 2c1c9f0d8aa6 msclust2.0.1.xml
--- a/msclust2.0.1.xml Thu Jan 16 13:12:07 2014 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,289 +0,0 @@
-
- Extracts fragmentation spectra from aligned data
-
-
- 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
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- ( summaryReport == True )
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-
-.. 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')
-
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