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Changeset 3:2c1c9f0d8aa6 (2014-01-17)

Previous changeset 2:a35b55bfe96c (2014-01-16) Next changeset 4:80075a4c6543 (2014-01-17)

Commit message:
using normal versioning

added:
msclust.xml

removed:
msclust2.0.1.xml

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

[

b'@@ -0,0 +1,289 @@\n+<tool name="MsClust" id="msclust2" version="2.0.2">\r\n+\t<description>Extracts fragmentation spectra from aligned data</description>\r\n+\t\r\n+\t<command interpreter="java -jar ">\r\n+\t MsClust.jar \r\n+\t \t-peaksFileName $inputPeaks \r\n+\t \t-dataType $dataType\r\n+ -imputationMethod $imputationMethod.type\r\n+ #if $imputationMethod.type == "valueRange"\r\n+ \t-rangeUpperLimit $imputationMethod.rangeUpperLimit\r\n+ #end if\r\n+\t\t-plInputFormat "metalign" \r\n+\t\t-potDensFuncType $potDensFuncType.type \r\n+\t\t-centerSelectionType $centerSelectionType.type \r\n+\t\t-clusteringType $clusteringType.type \r\n+\t\t-neighborhoodWindowSize $potDensFuncType.pdf_neighborhoodWindowSize \r\n+\t\t-clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion\r\n+\t\t-pearsonDistTreshold $potDensFuncType.pdf_pears_treshold\r\n+\t\t-pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf\r\n+\t\t-pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold\r\n+\t\t-pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope\r\n+\t\t-scanDistTol $potDensFuncType.pdf_scan_toler \r\n+\t\t-scanDistanceConfidence $potDensFuncType.pdf_scan_conf \r\n+\t\t-centrotypesOut $centrotypesOut \r\n+\t\t-simOut $simOut\r\n+\t\t-micOut $micOut\r\n+\t\t-mspOut $mspOut \r\n+\t\t-classOut $classOut\r\n+\t\t-outReport $htmlReportFile\r\n+\t -outReportPicturesPath $htmlReportFile.files_path\r\n+ #if $clusteringType.type == "fuzzyCMeans"\r\n+ \t-fcmMembershipWeightingExponent $clusteringType.fcmMembershipWeightingExponent \r\n+\t\t\t-fcmStopCriterion $clusteringType.fcmStopCriterion\r\n+\t\t\t-fcmCorrelationWeight $clusteringType.fcmCorrelationWeight\r\n+\t\t\t-fcmFinalAssemblyType $clusteringType.finalClusterAssembly.type\r\n+\t\t\t#if $clusteringType.finalClusterAssembly.type == "membershipBased"\r\n+\t\t\t\t-fcmMembershipCutoff $clusteringType.finalClusterAssembly.fcmMembershipCutoff\r\n+\t\t\t#end if\r\n+ #end if\r\n+\t\t-verbose "false"\r\n+\t #if $advancedSettings.settings == True\r\n+\t \t-advancedSettings YES\r\n+\t \t-saturationLimit $advancedSettings.saturationLimit\r\n+\t \t-sampleSelectionSortType $advancedSettings.sampleSelectionSortType\r\n+\t \t-simSelectionAlgorithm $advancedSettings.simSelectionAlgorithm\r\n+\t \t-simMassFilter "$advancedSettings.simMassFilter"\r\n+\t \t-simMembershipThreshold $advancedSettings.simMembershipThreshold\r\n+\t \t-simSaturationThreshold $advancedSettings.simSaturationThreshold\r\n+\t \t-simAbsenseThreshold $advancedSettings.simAbsenseThreshold\r\n+\t \t-micMembershipThreshold $advancedSettings.micMembershipThreshold\r\n+\t \t-peakIntensityCorrectionAlgorithm $advancedSettings.peakIntensityCorrectionAlgorithm\r\n+ #else\r\n+ \t-advancedSettings YES\r\n+ \t-sampleSelectionSortType SIM_INTENSITY\r\n+ \t-peakIntensityCorrectionAlgorithm CORRELATION_BASED\r\n+ #end if\r\n+\t \r\n+\t</command>\r\n+\t<inputs>\r\n+\t\r\n+\t \t<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />\r\n+\t\t<param name="dataType" type="select" size="30" label="Data type">\r\n+\t\t\t\t<option value="gcms" selected="true">GC-MS</option>\r\n+\t\t\t\t<option value="lcms">LC-MS</option>\r\n+\t\t\t</param>\r\n+\t \t<conditional name="imputationMethod">\r\n+\t\t\t<param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps">\r\n+\t\t\t\t<option value="none"'..b'n was used, this is the variation *after* pre-processing by MetAlign. \r\n+\r\n+*Peak Width confidence:* The higher the confidence, the stricter the threshold.\r\n+\r\n+*Correlation threshold (0.0 - 1.0):* Tolerance center for pearson distance calculation. The higher this value, \r\n+the higher the correlation between 2 items has to be for them to be considered \'close\'. \r\n+\r\n+*Correlation threshold confidence:* The higher the confidence, the stricter the threshold. `More...`__\r\n+\r\n+*Potential Density reduction (0.0 - 1.0):* Reduction tolerance center for pearson distance calculation. \r\n+The higher this value, the less the low correlated items get reduced, getting a chance to form a cluster of their own. \r\n+\r\n+*Potential Density reduction softness:* Reduction curve slope for pearson distance tolerance. Lower \r\n+values = stricter separation at the value determined in \'Potential Density reduction\' above \r\n+(TODO review this comment). \r\n+\r\n+*Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations \r\n+\r\n+.. __: javascript:window.open(\'$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\')\r\n+\r\n+\r\n+-----\r\n+\r\n+**Output files described below**\r\n+\r\n+-----\r\n+\r\n+*SPECTRA:* this file can be submitted to NIST for identification of the spectra.\r\n+\r\n+`Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_ \r\n+\r\n+.. _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\')\r\n+\r\n+-----\r\n+\r\n+*MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count \r\n+values (corrected by their membership) for all MEASURED cluster ions in the given sample.\r\n+\r\n+The MIC for a **cluster i** in **sample s**, where **cluster i** has **n** members is thus: \r\n+\r\n+sum ( [intensity of member n in **sample s**] x [membership value of member n in **cluster i** ] )\r\n+\r\n+-----\r\n+\r\n+*SIM:* stands for Selective Ion Mode -> it contains, for each cluster, the intensity values of the \r\n+most representative member ion peak of this cluster. The most representative member peak is the one with the \r\n+highest membership*average_intensity. This definition leads to conflicts as a peak can have a \r\n+membership in two or more clusters. The assignment of a SIM peak to a cluster depends on \r\n+the configured data type (LC or GC-MS). NB: this can be overruled in the "advanced settings":\r\n+\r\n+(1) LC-MS SIM: select SIM peak only once and for the centrotype in which this specific mass has its \r\n+highest membership; for neighboring centrotypes use its "second best SIM", etcetera. In other words,\r\n+if the SIM peak has been identified as the SIM in more than 1 cluster, assign as SIM to the cluster \r\n+with highest membership. Continue searching for other SIM peaks to assign to the other clusters until \r\n+all ambiguities are solved.\r\n+\r\n+(2) GC-MS SIM: the SIM peak can be "shared" by multiple clusters. However, the intensity values are corrected\r\n+by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not \r\n+"shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file. \r\n+\r\n+`Click here for more details on the SIM output file`_ \r\n+\r\n+.. _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\')\r\n+\r\n+\r\n+\r\n+ </help>\r\n+</tool>\r\n'

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

[

b'@@ -1,289 +0,0 @@\n-<tool name="MsClust" id="msclust2" version="2.0.1">\r\n-\t<description>Extracts fragmentation spectra from aligned data</description>\r\n-\t\r\n-\t<command interpreter="java -jar ">\r\n-\t MsClust.jar \r\n-\t \t-peaksFileName $inputPeaks \r\n-\t \t-dataType $dataType\r\n- -imputationMethod $imputationMethod.type\r\n- #if $imputationMethod.type == "valueRange"\r\n- \t-rangeUpperLimit $imputationMethod.rangeUpperLimit\r\n- #end if\r\n-\t\t-plInputFormat "metalign" \r\n-\t\t-potDensFuncType $potDensFuncType.type \r\n-\t\t-centerSelectionType $centerSelectionType.type \r\n-\t\t-clusteringType $clusteringType.type \r\n-\t\t-neighborhoodWindowSize $potDensFuncType.pdf_neighborhoodWindowSize \r\n-\t\t-clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion\r\n-\t\t-pearsonDistTreshold $potDensFuncType.pdf_pears_treshold\r\n-\t\t-pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf\r\n-\t\t-pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold\r\n-\t\t-pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope\r\n-\t\t-scanDistTol $potDensFuncType.pdf_scan_toler \r\n-\t\t-scanDistanceConfidence $potDensFuncType.pdf_scan_conf \r\n-\t\t-centrotypesOut $centrotypesOut \r\n-\t\t-simOut $simOut\r\n-\t\t-micOut $micOut\r\n-\t\t-mspOut $mspOut \r\n-\t\t-classOut $classOut\r\n-\t\t-outReport $htmlReportFile\r\n-\t -outReportPicturesPath $htmlReportFile.files_path\r\n- #if $clusteringType.type == "fuzzyCMeans"\r\n- \t-fcmMembershipWeightingExponent $clusteringType.fcmMembershipWeightingExponent \r\n-\t\t\t-fcmStopCriterion $clusteringType.fcmStopCriterion\r\n-\t\t\t-fcmCorrelationWeight $clusteringType.fcmCorrelationWeight\r\n-\t\t\t-fcmFinalAssemblyType $clusteringType.finalClusterAssembly.type\r\n-\t\t\t#if $clusteringType.finalClusterAssembly.type == "membershipBased"\r\n-\t\t\t\t-fcmMembershipCutoff $clusteringType.finalClusterAssembly.fcmMembershipCutoff\r\n-\t\t\t#end if\r\n- #end if\r\n-\t\t-verbose "false"\r\n-\t #if $advancedSettings.settings == True\r\n-\t \t-advancedSettings YES\r\n-\t \t-saturationLimit $advancedSettings.saturationLimit\r\n-\t \t-sampleSelectionSortType $advancedSettings.sampleSelectionSortType\r\n-\t \t-simSelectionAlgorithm $advancedSettings.simSelectionAlgorithm\r\n-\t \t-simMassFilter "$advancedSettings.simMassFilter"\r\n-\t \t-simMembershipThreshold $advancedSettings.simMembershipThreshold\r\n-\t \t-simSaturationThreshold $advancedSettings.simSaturationThreshold\r\n-\t \t-simAbsenseThreshold $advancedSettings.simAbsenseThreshold\r\n-\t \t-micMembershipThreshold $advancedSettings.micMembershipThreshold\r\n-\t \t-peakIntensityCorrectionAlgorithm $advancedSettings.peakIntensityCorrectionAlgorithm\r\n- #else\r\n- \t-advancedSettings YES\r\n- \t-sampleSelectionSortType SIM_INTENSITY\r\n- \t-peakIntensityCorrectionAlgorithm CORRELATION_BASED\r\n- #end if\r\n-\t \r\n-\t</command>\r\n-\t<inputs>\r\n-\t\r\n-\t \t<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />\r\n-\t\t<param name="dataType" type="select" size="30" label="Data type">\r\n-\t\t\t\t<option value="gcms" selected="true">GC-MS</option>\r\n-\t\t\t\t<option value="lcms">LC-MS</option>\r\n-\t\t\t</param>\r\n-\t \t<conditional name="imputationMethod">\r\n-\t\t\t<param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps">\r\n-\t\t\t\t<option value="none"'..b'n was used, this is the variation *after* pre-processing by MetAlign. \r\n-\r\n-*Peak Width confidence:* The higher the confidence, the stricter the threshold.\r\n-\r\n-*Correlation threshold (0.0 - 1.0):* Tolerance center for pearson distance calculation. The higher this value, \r\n-the higher the correlation between 2 items has to be for them to be considered \'close\'. \r\n-\r\n-*Correlation threshold confidence:* The higher the confidence, the stricter the threshold. `More...`__\r\n-\r\n-*Potential Density reduction (0.0 - 1.0):* Reduction tolerance center for pearson distance calculation. \r\n-The higher this value, the less the low correlated items get reduced, getting a chance to form a cluster of their own. \r\n-\r\n-*Potential Density reduction softness:* Reduction curve slope for pearson distance tolerance. Lower \r\n-values = stricter separation at the value determined in \'Potential Density reduction\' above \r\n-(TODO review this comment). \r\n-\r\n-*Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations \r\n-\r\n-.. __: javascript:window.open(\'$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\')\r\n-\r\n-\r\n------\r\n-\r\n-**Output files described below**\r\n-\r\n------\r\n-\r\n-*SPECTRA:* this file can be submitted to NIST for identification of the spectra.\r\n-\r\n-`Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_ \r\n-\r\n-.. _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\')\r\n-\r\n------\r\n-\r\n-*MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count \r\n-values (corrected by their membership) for all MEASURED cluster ions in the given sample.\r\n-\r\n-The MIC for a **cluster i** in **sample s**, where **cluster i** has **n** members is thus: \r\n-\r\n-sum ( [intensity of member n in **sample s**] x [membership value of member n in **cluster i** ] )\r\n-\r\n------\r\n-\r\n-*SIM:* stands for Selective Ion Mode -> it contains, for each cluster, the intensity values of the \r\n-most representative member ion peak of this cluster. The most representative member peak is the one with the \r\n-highest membership*average_intensity. This definition leads to conflicts as a peak can have a \r\n-membership in two or more clusters. The assignment of a SIM peak to a cluster depends on \r\n-the configured data type (LC or GC-MS). NB: this can be overruled in the "advanced settings":\r\n-\r\n-(1) LC-MS SIM: select SIM peak only once and for the centrotype in which this specific mass has its \r\n-highest membership; for neighboring centrotypes use its "second best SIM", etcetera. In other words,\r\n-if the SIM peak has been identified as the SIM in more than 1 cluster, assign as SIM to the cluster \r\n-with highest membership. Continue searching for other SIM peaks to assign to the other clusters until \r\n-all ambiguities are solved.\r\n-\r\n-(2) GC-MS SIM: the SIM peak can be "shared" by multiple clusters. However, the intensity values are corrected\r\n-by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not \r\n-"shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file. \r\n-\r\n-`Click here for more details on the SIM output file`_ \r\n-\r\n-.. _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\')\r\n-\r\n-\r\n-\r\n- </help>\r\n-</tool>\r\n'