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11
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1 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
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2 <param name="logging" type="select" label="logging, logical" value="1">
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3 <option value="True">True</option>
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4 <option value="False">False</option>
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5 </param>
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6 <param name="email" type="text" label="email, character" value=""/>
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7 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
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8 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
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9 <option value="True">True</option>
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10 <option value="False">False</option>
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11 </param>
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12 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
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13 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
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14 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
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15 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
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16 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
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17 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
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18 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
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19 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
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20 <option value="True">True</option>
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21 <option value="False">False</option>
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22 </param>
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23 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
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24 <option value="True">True</option>
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25 <option value="False">False</option>
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26 </param>
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27 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
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28 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
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29 <option value="True">True</option>
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30 <option value="False">False</option>
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31 </param>
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32 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
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33 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=" "/>
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34 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
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35 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
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36 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
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37 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/>
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38 <param name="normalizationSubtractBackground" type="select" label="normalization.subtract.background, logical" value="0">
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39 <option value="True">True</option>
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40 <option value="False">False</option>
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41 </param>
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42 <param name="qc" type="select" label="qc, logical" value="1">
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43 <option value="True">True</option>
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44 <option value="False">False</option>
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45 </param>
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46 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
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47 <option value="True">True</option>
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48 <option value="False">False</option>
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49 </param>
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50 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
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51 <option value="True">True</option>
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52 <option value="False">False</option>
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53 </param>
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54 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
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55 <option value="True">True</option>
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56 <option value="False">False</option>
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57 </param>
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58 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
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59 <option value="True">True</option>
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60 <option value="False">False</option>
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61 </param>
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62 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
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63 <option value="True">True</option>
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64 <option value="False">False</option>
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65 </param>
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66 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
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67 <option value="True">True</option>
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68 <option value="False">False</option>
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69 </param>
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70 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/>
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71 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
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72 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
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73 <option value="True">True</option>
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74 <option value="False">False</option>
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75 </param>
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76 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
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77 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
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78 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
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79 <option value="True">True</option>
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80 <option value="False">False</option>
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81 </param>
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82 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
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83 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
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84 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
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85 <option value="True">True</option>
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86 <option value="False">False</option>
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87 </param>
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88 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
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89 <option value="True">True</option>
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90 <option value="False">False</option>
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91 </param>
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92 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
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93 <option value="True">True</option>
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94 <option value="False">False</option>
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95 </param>
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96 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
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97 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
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98 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
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99 <param name="batch" type="select" label="batch, logical" value="1">
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100 <option value="True">True</option>
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101 <option value="False">False</option>
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102 </param>
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103 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
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104 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
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105 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
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106 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
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107 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
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108 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
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109 <option value="True">True</option>
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110 <option value="False">False</option>
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111 </param>
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112 <param name="profiles" type="select" label="profiles, logical" value="1">
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113 <option value="True">True</option>
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114 <option value="False">False</option>
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115 </param>
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116 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
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117 <option value="True">True</option>
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118 <option value="False">False</option>
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119 </param>
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120 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
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121 <option value="True">True</option>
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122 <option value="False">False</option>
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123 </param>
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124 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
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125 <option value="True">True</option>
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126 <option value="False">False</option>
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127 </param>
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128 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
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129 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
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130 <option value="True">True</option>
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131 <option value="False">False</option>
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132 </param>
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133 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
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134 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
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135 <param name="differential" type="select" label="differential, logical" value="1">
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136 <option value="True">True</option>
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137 <option value="False">False</option>
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138 </param>
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139 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
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140 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
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141 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
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142 <option value="True">True</option>
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143 <option value="False">False</option>
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144 </param>
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145 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
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146 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
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147 <option value="True">True</option>
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148 <option value="False">False</option>
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149 </param>
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150 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
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151 <option value="True">True</option>
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152 <option value="False">False</option>
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153 </param>
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154 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
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155 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
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156 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
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157 <option value="True">True</option>
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158 <option value="False">False</option>
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159 </param>
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160 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
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161 <option value="True">True</option>
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162 <option value="False">False</option>
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163 </param>
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