Mercurial > repos > pavlo-lutsik > rnbeads
comparison automated.option.assignments.txt @ 8:7bc6e673c8e8 draft
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| author | pavlo-lutsik |
|---|---|
| date | Thu, 18 Apr 2013 07:36:36 -0400 |
| parents | |
| children |
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| 7:a1c96ef6c111 | 8:7bc6e673c8e8 |
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| 1 #if str( $options.analysisName ) != "" | |
| 2 --analysis-name="$options.analysisName" | |
| 3 #end if | |
| 4 #if str( $options.logging ) == "True" | |
| 5 --logging | |
| 6 #end if | |
| 7 #if str( $options.email ) != "" | |
| 8 --email="$options.email" | |
| 9 #end if | |
| 10 #if str( $options.assembly ) != "" | |
| 11 --assembly="$options.assembly" | |
| 12 #end if | |
| 13 #if str( $options.analyzeSites ) == "True" | |
| 14 --analyze-sites | |
| 15 #end if | |
| 16 #if str( $options.regionTypes ) != "" | |
| 17 --region-types="$options.regionTypes" | |
| 18 #end if | |
| 19 #if str( $options.identifiersColumn ) != "" | |
| 20 --identifiers-column="$options.identifiersColumn" | |
| 21 #end if | |
| 22 #if str( $options.pointsCategory ) != "" | |
| 23 --points-category="$options.pointsCategory" | |
| 24 #end if | |
| 25 #if str( $options.colorsCategory ) != "" | |
| 26 --colors-category="$options.colorsCategory" | |
| 27 #end if | |
| 28 #if str( $options.colorsGradient ) != "" | |
| 29 --colors-gradient="$options.colorsGradient" | |
| 30 #end if | |
| 31 #if str( $options.minGroupSize ) != "" | |
| 32 --min-group-size="$options.minGroupSize" | |
| 33 #end if | |
| 34 #if str( $options.maxGroupCount ) != "" | |
| 35 --max-group-count="$options.maxGroupCount" | |
| 36 #end if | |
| 37 #if str( $options.gzLargeFiles ) == "True" | |
| 38 --gz-large-files | |
| 39 #end if | |
| 40 #if str( $options.strandSpecific ) == "True" | |
| 41 --strand-specific | |
| 42 #end if | |
| 43 #if str( $options.replicateIdColumn ) != "" | |
| 44 --replicate-id-column="$options.replicateIdColumn" | |
| 45 #end if | |
| 46 #if str( $options.loadingNormalization ) == "True" | |
| 47 --loading-normalization | |
| 48 #end if | |
| 49 #if str( $options.loadingDefaultDataType ) != "" | |
| 50 --loading-default-data-type="$options.loadingDefaultDataType" | |
| 51 #end if | |
| 52 #if str( $options.loadingTableSeparator ) != "" | |
| 53 --loading-table-separator="$options.loadingTableSeparator" | |
| 54 #end if | |
| 55 #if str( $options.loadingBedStyle ) != "" | |
| 56 --loading-bed-style="$options.loadingBedStyle" | |
| 57 #end if | |
| 58 #if str( $options.loadingBedColumns ) != "" | |
| 59 --loading-bed-columns="$options.loadingBedColumns" | |
| 60 #end if | |
| 61 #if str( $options.loadingBedFrameShift ) != "" | |
| 62 --loading-bed-frame-shift="$options.loadingBedFrameShift" | |
| 63 #end if | |
| 64 #if str( $options.normalizationMethod ) != "" | |
| 65 --normalization-method="$options.normalizationMethod" | |
| 66 #end if | |
| 67 #if str( $options.normalizationSubtractBackground ) == "True" | |
| 68 --normalization-subtract-background | |
| 69 #end if | |
| 70 #if str( $options.qc ) == "True" | |
| 71 --qc | |
| 72 #end if | |
| 73 #if str( $options.qcBoxplots ) == "True" | |
| 74 --qc-boxplots | |
| 75 #end if | |
| 76 #if str( $options.qcBarplots ) == "True" | |
| 77 --qc-barplots | |
| 78 #end if | |
| 79 #if str( $options.qcNegativeBoxplot ) == "True" | |
| 80 --qc-negative-boxplot | |
| 81 #end if | |
| 82 #if str( $options.qcSnpHeatmap ) == "True" | |
| 83 --qc-snp-heatmap | |
| 84 #end if | |
| 85 #if str( $options.qcSnpBoxplot ) == "True" | |
| 86 --qc-snp-boxplot | |
| 87 #end if | |
| 88 #if str( $options.qcSnpBarplot ) == "True" | |
| 89 --qc-snp-barplot | |
| 90 #end if | |
| 91 #if str( $options.qcSampleBatchSize ) != "" | |
| 92 --qc-sample-batch-size="$options.qcSampleBatchSize" | |
| 93 #end if | |
| 94 #if str( $options.filteringContextRemoval ) != "" | |
| 95 --filtering-context-removal="$options.filteringContextRemoval" | |
| 96 #end if | |
| 97 #if str( $options.filteringSnp ) == "True" | |
| 98 --filtering-snp | |
| 99 #end if | |
| 100 #if str( $options.filteringSnpFrequency ) != "" | |
| 101 --filtering-snp-frequency="$options.filteringSnpFrequency" | |
| 102 #end if | |
| 103 #if str( $options.filteringSnpAccepted ) != "" | |
| 104 --filtering-snp-accepted="$options.filteringSnpAccepted" | |
| 105 #end if | |
| 106 #if str( $options.filteringSexChromosomesRemoval ) == "True" | |
| 107 --filtering-sex-chromosomes-removal | |
| 108 #end if | |
| 109 #if str( $options.filteringMissingValueQuantile ) != "" | |
| 110 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile" | |
| 111 #end if | |
| 112 #if str( $options.filteringCoverageThreshold ) != "" | |
| 113 --filtering-coverage-threshold="$options.filteringCoverageThreshold" | |
| 114 #end if | |
| 115 #if str( $options.filteringLowCoverageMasking ) == "True" | |
| 116 --filtering-low-coverage-masking | |
| 117 #end if | |
| 118 #if str( $options.filteringHighCoverageOutliers ) == "True" | |
| 119 --filtering-high-coverage-outliers | |
| 120 #end if | |
| 121 #if str( $options.filteringGreedycut ) == "True" | |
| 122 --filtering-greedycut | |
| 123 #end if | |
| 124 #if str( $options.filteringGreedycutPvalueThreshold ) != "" | |
| 125 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" | |
| 126 #end if | |
| 127 #if str( $options.filteringGreedycutRcTies ) != "" | |
| 128 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" | |
| 129 #end if | |
| 130 #if str( $options.filteringDeviationThreshold ) != "" | |
| 131 --filtering-deviation-threshold="$options.filteringDeviationThreshold" | |
| 132 #end if | |
| 133 #if str( $options.batch ) == "True" | |
| 134 --batch | |
| 135 #end if | |
| 136 #if str( $options.batchDreductionColumns ) != "" | |
| 137 --batch-dreduction-columns="$options.batchDreductionColumns" | |
| 138 #end if | |
| 139 #if str( $options.batchPrincipalComponents ) != "" | |
| 140 --batch-principal-components="$options.batchPrincipalComponents" | |
| 141 #end if | |
| 142 #if str( $options.batchCorrelationColumns ) != "" | |
| 143 --batch-correlation-columns="$options.batchCorrelationColumns" | |
| 144 #end if | |
| 145 #if str( $options.batchCorrelationPvalueThreshold ) != "" | |
| 146 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" | |
| 147 #end if | |
| 148 #if str( $options.batchCorrelationPermutations ) != "" | |
| 149 --batch-correlation-permutations="$options.batchCorrelationPermutations" | |
| 150 #end if | |
| 151 #if str( $options.batchCorrelationQc ) == "True" | |
| 152 --batch-correlation-qc | |
| 153 #end if | |
| 154 #if str( $options.profiles ) == "True" | |
| 155 --profiles | |
| 156 #end if | |
| 157 #if str( $options.profilesBetaDistribution ) == "True" | |
| 158 --profiles-beta-distribution | |
| 159 #end if | |
| 160 #if str( $options.profilesIntersample ) == "True" | |
| 161 --profiles-intersample | |
| 162 #end if | |
| 163 #if str( $options.profilesDeviationPlots ) == "True" | |
| 164 --profiles-deviation-plots | |
| 165 #end if | |
| 166 #if str( $options.profilesColumns ) != "" | |
| 167 --profiles-columns="$options.profilesColumns" | |
| 168 #end if | |
| 169 #if str( $options.profilesClustering ) == "True" | |
| 170 --profiles-clustering | |
| 171 #end if | |
| 172 #if str( $options.profilesClusteringTopProbes ) != "" | |
| 173 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes" | |
| 174 #end if | |
| 175 #if str( $options.regionProfilesTypes ) != "" | |
| 176 --region-profiles-types="$options.regionProfilesTypes" | |
| 177 #end if | |
| 178 #if str( $options.differential ) == "True" | |
| 179 --differential | |
| 180 #end if | |
| 181 #if str( $options.differentialPermutations ) != "" | |
| 182 --differential-permutations="$options.differentialPermutations" | |
| 183 #end if | |
| 184 #if str( $options.differentialComparisonColumns ) != "" | |
| 185 --differential-comparison-columns="$options.differentialComparisonColumns" | |
| 186 #end if | |
| 187 #if str( $options.differentialEnrichment ) == "True" | |
| 188 --differential-enrichment | |
| 189 #end if | |
| 190 #if str( $options.exportToUcsc ) != "" | |
| 191 --export-to-ucsc="$options.exportToUcsc" | |
| 192 #end if | |
| 193 #if str( $options.exportToBed ) == "True" | |
| 194 --export-to-bed | |
| 195 #end if | |
| 196 #if str( $options.exportToCsv ) == "True" | |
| 197 --export-to-csv | |
| 198 #end if | |
| 199 #if str( $options.exportTypes ) != "" | |
| 200 --export-types="$options.exportTypes" | |
| 201 #end if | |
| 202 #if str( $options.colors3Gradient ) != "" | |
| 203 --colors-3-gradient="$options.colors3Gradient" | |
| 204 #end if | |
| 205 #if str( $options.loggingMemory ) == "True" | |
| 206 --logging-memory | |
| 207 #end if | |
| 208 #if str( $options.usePstoimg ) == "True" | |
| 209 --use-pstoimg | |
| 210 #end if |