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