| Previous changeset 8:7bc6e673c8e8 (2013-04-18) Next changeset 10:945690943560 (2013-04-20) |
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Commit message:
Deleted selected files |
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removed:
automated.option.assignments.txt |
| b |
| diff -r 7bc6e673c8e8 -r 68db09d2e2a4 automated.option.assignments.txt --- a/automated.option.assignments.txt Thu Apr 18 07:36:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,210 +0,0 @@ - #if str( $options.analysisName ) != "" - --analysis-name="$options.analysisName" - #end if - #if str( $options.logging ) == "True" - --logging - #end if - #if str( $options.email ) != "" - --email="$options.email" - #end if - #if str( $options.assembly ) != "" - --assembly="$options.assembly" - #end if - #if str( $options.analyzeSites ) == "True" - --analyze-sites - #end if - #if str( $options.regionTypes ) != "" - --region-types="$options.regionTypes" - #end if - #if str( $options.identifiersColumn ) != "" - --identifiers-column="$options.identifiersColumn" - #end if - #if str( $options.pointsCategory ) != "" - --points-category="$options.pointsCategory" - #end if - #if str( $options.colorsCategory ) != "" - --colors-category="$options.colorsCategory" - #end if - #if str( $options.colorsGradient ) != "" - --colors-gradient="$options.colorsGradient" - #end if - #if str( $options.minGroupSize ) != "" - --min-group-size="$options.minGroupSize" - #end if - #if str( $options.maxGroupCount ) != "" - --max-group-count="$options.maxGroupCount" - #end if - #if str( $options.gzLargeFiles ) == "True" - --gz-large-files - #end if - #if str( $options.strandSpecific ) == "True" - --strand-specific - #end if - #if str( $options.replicateIdColumn ) != "" - --replicate-id-column="$options.replicateIdColumn" - #end if - #if str( $options.loadingNormalization ) == "True" - --loading-normalization - #end if - #if str( $options.loadingDefaultDataType ) != "" - --loading-default-data-type="$options.loadingDefaultDataType" - #end if - #if str( $options.loadingTableSeparator ) != "" - --loading-table-separator="$options.loadingTableSeparator" - #end if - #if str( $options.loadingBedStyle ) != "" - --loading-bed-style="$options.loadingBedStyle" - #end if - #if str( $options.loadingBedColumns ) != "" - --loading-bed-columns="$options.loadingBedColumns" - #end if - #if str( $options.loadingBedFrameShift ) != "" - --loading-bed-frame-shift="$options.loadingBedFrameShift" - #end if - #if str( $options.normalizationMethod ) != "" - --normalization-method="$options.normalizationMethod" - #end if - #if str( $options.normalizationSubtractBackground ) == "True" - --normalization-subtract-background - #end if - #if str( $options.qc ) == "True" - --qc - #end if - #if str( $options.qcBoxplots ) == "True" - --qc-boxplots - #end if - #if str( $options.qcBarplots ) == "True" - --qc-barplots - #end if - #if str( $options.qcNegativeBoxplot ) == "True" - --qc-negative-boxplot - #end if - #if str( $options.qcSnpHeatmap ) == "True" - --qc-snp-heatmap - #end if - #if str( $options.qcSnpBoxplot ) == "True" - --qc-snp-boxplot - #end if - #if str( $options.qcSnpBarplot ) == "True" - --qc-snp-barplot - #end if - #if str( $options.qcSampleBatchSize ) != "" - --qc-sample-batch-size="$options.qcSampleBatchSize" - #end if - #if str( $options.filteringContextRemoval ) != "" - --filtering-context-removal="$options.filteringContextRemoval" - #end if - #if str( $options.filteringSnp ) == "True" - --filtering-snp - #end if - #if str( $options.filteringSnpFrequency ) != "" - --filtering-snp-frequency="$options.filteringSnpFrequency" - #end if - #if str( $options.filteringSnpAccepted ) != "" - --filtering-snp-accepted="$options.filteringSnpAccepted" - #end if - #if str( $options.filteringSexChromosomesRemoval ) == "True" - --filtering-sex-chromosomes-removal - #end if - #if str( $options.filteringMissingValueQuantile ) != "" - --filtering-missing-value-quantile="$options.filteringMissingValueQuantile" - #end if - #if str( $options.filteringCoverageThreshold ) != "" - --filtering-coverage-threshold="$options.filteringCoverageThreshold" - #end if - #if str( $options.filteringLowCoverageMasking ) == "True" - --filtering-low-coverage-masking - #end if - #if str( $options.filteringHighCoverageOutliers ) == "True" - --filtering-high-coverage-outliers - #end if - #if str( $options.filteringGreedycut ) == "True" - --filtering-greedycut - #end if - #if str( $options.filteringGreedycutPvalueThreshold ) != "" - --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" - #end if - #if str( $options.filteringGreedycutRcTies ) != "" - --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" - #end if - #if str( $options.filteringDeviationThreshold ) != "" - --filtering-deviation-threshold="$options.filteringDeviationThreshold" - #end if - #if str( $options.batch ) == "True" - --batch - #end if - #if str( $options.batchDreductionColumns ) != "" - --batch-dreduction-columns="$options.batchDreductionColumns" - #end if - #if str( $options.batchPrincipalComponents ) != "" - --batch-principal-components="$options.batchPrincipalComponents" - #end if - #if str( $options.batchCorrelationColumns ) != "" - --batch-correlation-columns="$options.batchCorrelationColumns" - #end if - #if str( $options.batchCorrelationPvalueThreshold ) != "" - --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" - #end if - #if str( $options.batchCorrelationPermutations ) != "" - --batch-correlation-permutations="$options.batchCorrelationPermutations" - #end if - #if str( $options.batchCorrelationQc ) == "True" - --batch-correlation-qc - #end if - #if str( $options.profiles ) == "True" - --profiles - #end if - #if str( $options.profilesBetaDistribution ) == "True" - --profiles-beta-distribution - #end if - #if str( $options.profilesIntersample ) == "True" - --profiles-intersample - #end if - #if str( $options.profilesDeviationPlots ) == "True" - --profiles-deviation-plots - #end if - #if str( $options.profilesColumns ) != "" - --profiles-columns="$options.profilesColumns" - #end if - #if str( $options.profilesClustering ) == "True" - --profiles-clustering - #end if - #if str( $options.profilesClusteringTopProbes ) != "" - --profiles-clustering-top-probes="$options.profilesClusteringTopProbes" - #end if - #if str( $options.regionProfilesTypes ) != "" - --region-profiles-types="$options.regionProfilesTypes" - #end if - #if str( $options.differential ) == "True" - --differential - #end if - #if str( $options.differentialPermutations ) != "" - --differential-permutations="$options.differentialPermutations" - #end if - #if str( $options.differentialComparisonColumns ) != "" - --differential-comparison-columns="$options.differentialComparisonColumns" - #end if - #if str( $options.differentialEnrichment ) == "True" - --differential-enrichment - #end if - #if str( $options.exportToUcsc ) != "" - --export-to-ucsc="$options.exportToUcsc" - #end if - #if str( $options.exportToBed ) == "True" - --export-to-bed - #end if - #if str( $options.exportToCsv ) == "True" - --export-to-csv - #end if - #if str( $options.exportTypes ) != "" - --export-types="$options.exportTypes" - #end if - #if str( $options.colors3Gradient ) != "" - --colors-3-gradient="$options.colors3Gradient" - #end if - #if str( $options.loggingMemory ) == "True" - --logging-memory - #end if - #if str( $options.usePstoimg ) == "True" - --use-pstoimg - #end if \ No newline at end of file |