changeset 9:68db09d2e2a4 draft

Deleted selected files
author pavlo-lutsik
date Thu, 18 Apr 2013 07:38:46 -0400
parents 7bc6e673c8e8
children 945690943560
files automated.option.assignments.txt
diffstat 1 files changed, 0 insertions(+), 210 deletions(-) [+]
line wrap: on
line diff
--- a/automated.option.assignments.txt	Thu Apr 18 07:36:36 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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