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1 <?xml version="0.9"?>
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2 <tool id="rnbeads" name="RnBeads" version="0.9">
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3 <description>Performs RnBeads analysis for the selected set of </description>
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4 <requirements>
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5 <requirement type="set_environment" version="1.0">R_SCRIPTS_PATH</requirement>
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6 <requirement type="package" version="3.0.0">R</requirement>
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7 </requirements>
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8 <command interpreter="bash">rnbeads_galaxy_wrapper.sh
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9 --report-dir="$html_file.extra_files_path"
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10 --output-file="$html_file"
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11 #if str( $inputDataSelector.dataType ) == "idats"
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12 --pheno="$inputDataSelector.sampleAnnotations"
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13 #end if
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14 #if str( $inputDataSelector.dataType ) != "idats"
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15 #pass
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16 #else if str( $inputDataSelector.idatSelector.idatSource ) == "history"
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17 --data-type="idatFiles"
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18 #set $idatList=""
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19 #for $input_file in $inputDataSelector.idatSelector.idatSeries:
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20 #set $idatList+=str( $input_file.idatFile )
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21 #set $idatList+=","
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22 #end for
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23 --idat-files="$idatList"
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24 #else:
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25 --data-type="idatDir"
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26 --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path"
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27 #end if
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28 #if str( $inputDataSelector.dataType ) == "gsreport"
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29 --data-type="GS.report"
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30 --gs-report="$inputDataSelector.gsReportFile"
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31 #end if
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32 #if str( $inputDataSelector.dataType ) == "geo"
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33 --data-type="GEO"
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34 --geo-series=$inputDataSelector.geoSeries
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35 #end if
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36 #if str( $inputDataSelector.dataType ) == "tables"
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37 --data-type="data.files"
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38 --pheno="$inputDataSelector.sampleAnnotations"
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39 #end if
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40 #if str( $inputDataSelector.dataType ) == "tables"
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41 --data-type="data.files"
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42 --pheno="$inputDataSelector.sampleAnnotations"
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43 --betas="$inputDataSelector.betaTable"
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44 --pvals="$inputDataSelector.pvalTable"
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45 #end if
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46 #if str( $inputDataSelector.dataType ) == "bed"
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47 --data-type="bed.dir"
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48 --pheno="$inputDataSelector.sampleAnnotations"
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49 #set $bedList=""
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50 #for $input_file in $inputDataSelector.bedSeries:
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51 #set $bedList+=str( $input_file.bedFile )
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52 #set $bedList+=","
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53 #end for
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54 --bed-files="$bedList"
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55 #end if
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56 #if str( $options.optionSet ) == "full"
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57 #if str( $options.analysisName ) != ""
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58 --analysis-name="$options.analysisName"
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59 #end if
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60 #if str( $options.logging ) == "True"
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61 --logging
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62 #end if
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63 #if str( $options.email ) != ""
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64 --email="$options.email"
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65 #end if
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66 #if str( $options.assembly ) != ""
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67 --assembly="$options.assembly"
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68 #end if
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69 #if str( $options.analyzeSites ) == "True"
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70 --analyze-sites
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71 #end if
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72 #if str( $options.regionTypes ) != ""
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73 --region-types="$options.regionTypes"
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74 #end if
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75 #if str( $options.identifiersColumn ) != ""
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76 --identifiers-column="$options.identifiersColumn"
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77 #end if
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78 #if str( $options.pointsCategory ) != ""
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79 --points-category="$options.pointsCategory"
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80 #end if
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81 #if str( $options.colorsCategory ) != ""
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82 --colors-category="$options.colorsCategory"
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83 #end if
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84 #if str( $options.colorsGradient ) != ""
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85 --colors-gradient="$options.colorsGradient"
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86 #end if
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87 #if str( $options.minGroupSize ) != ""
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88 --min-group-size="$options.minGroupSize"
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89 #end if
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90 #if str( $options.maxGroupCount ) != ""
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91 --max-group-count="$options.maxGroupCount"
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92 #end if
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93 #if str( $options.gzLargeFiles ) == "True"
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94 --gz-large-files
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95 #end if
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96 #if str( $options.strandSpecific ) == "True"
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97 --strand-specific
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98 #end if
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99 #if str( $options.replicateIdColumn ) != ""
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100 --replicate-id-column="$options.replicateIdColumn"
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101 #end if
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102 #if str( $options.loadingNormalization ) == "True"
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103 --loading-normalization
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104 #end if
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105 #if str( $options.loadingDefaultDataType ) != ""
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106 --loading-default-data-type="$options.loadingDefaultDataType"
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107 #end if
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108 #if str( $options.loadingTableSeparator ) != ""
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109 --loading-table-separator="$options.loadingTableSeparator"
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110 #end if
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111 #if str( $options.loadingBedStyle ) != ""
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112 --loading-bed-style="$options.loadingBedStyle"
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113 #end if
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114 #if str( $options.loadingBedColumns ) != ""
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115 --loading-bed-columns="$options.loadingBedColumns"
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116 #end if
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117 #if str( $options.loadingBedFrameShift ) != ""
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118 --loading-bed-frame-shift="$options.loadingBedFrameShift"
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119 #end if
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120 #if str( $options.normalizationMethod ) != ""
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121 --normalization-method="$options.normalizationMethod"
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122 #end if
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123 #if str( $options.normalizationSubtractBackground ) == "True"
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124 --normalization-subtract-background
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125 #end if
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126 #if str( $options.qc ) == "True"
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127 --qc
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128 #end if
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129 #if str( $options.qcBoxplots ) == "True"
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130 --qc-boxplots
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131 #end if
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132 #if str( $options.qcBarplots ) == "True"
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133 --qc-barplots
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134 #end if
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135 #if str( $options.qcNegativeBoxplot ) == "True"
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136 --qc-negative-boxplot
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137 #end if
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138 #if str( $options.qcSnpHeatmap ) == "True"
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139 --qc-snp-heatmap
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140 #end if
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141 #if str( $options.qcSnpBoxplot ) == "True"
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142 --qc-snp-boxplot
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143 #end if
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144 #if str( $options.qcSnpBarplot ) == "True"
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145 --qc-snp-barplot
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146 #end if
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147 #if str( $options.qcSampleBatchSize ) != ""
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148 --qc-sample-batch-size="$options.qcSampleBatchSize"
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149 #end if
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150 #if str( $options.filteringContextRemoval ) != ""
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151 --filtering-context-removal="$options.filteringContextRemoval"
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152 #end if
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153 #if str( $options.filteringSnp ) == "True"
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154 --filtering-snp
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155 #end if
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156 #if str( $options.filteringSnpFrequency ) != ""
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157 --filtering-snp-frequency="$options.filteringSnpFrequency"
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158 #end if
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159 #if str( $options.filteringSnpAccepted ) != ""
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160 --filtering-snp-accepted="$options.filteringSnpAccepted"
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161 #end if
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162 #if str( $options.filteringSexChromosomesRemoval ) == "True"
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163 --filtering-sex-chromosomes-removal
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164 #end if
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165 #if str( $options.filteringMissingValueQuantile ) != ""
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166 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
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167 #end if
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168 #if str( $options.filteringCoverageThreshold ) != ""
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169 --filtering-coverage-threshold="$options.filteringCoverageThreshold"
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170 #end if
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171 #if str( $options.filteringLowCoverageMasking ) == "True"
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172 --filtering-low-coverage-masking
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173 #end if
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174 #if str( $options.filteringHighCoverageOutliers ) == "True"
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175 --filtering-high-coverage-outliers
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176 #end if
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177 #if str( $options.filteringGreedycut ) == "True"
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178 --filtering-greedycut
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179 #end if
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180 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
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181 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
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182 #end if
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183 #if str( $options.filteringGreedycutRcTies ) != ""
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184 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
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185 #end if
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186 #if str( $options.filteringDeviationThreshold ) != ""
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187 --filtering-deviation-threshold="$options.filteringDeviationThreshold"
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188 #end if
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189 #if str( $options.batch ) == "True"
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190 --batch
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191 #end if
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192 #if str( $options.batchDreductionColumns ) != ""
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193 --batch-dreduction-columns="$options.batchDreductionColumns"
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194 #end if
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195 #if str( $options.batchPrincipalComponents ) != ""
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196 --batch-principal-components="$options.batchPrincipalComponents"
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197 #end if
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198 #if str( $options.batchCorrelationColumns ) != ""
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199 --batch-correlation-columns="$options.batchCorrelationColumns"
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200 #end if
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201 #if str( $options.batchCorrelationPvalueThreshold ) != ""
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202 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold"
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203 #end if
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204 #if str( $options.batchCorrelationPermutations ) != ""
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205 --batch-correlation-permutations="$options.batchCorrelationPermutations"
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206 #end if
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207 #if str( $options.batchCorrelationQc ) == "True"
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208 --batch-correlation-qc
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209 #end if
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210 #if str( $options.profiles ) == "True"
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211 --profiles
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212 #end if
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213 #if str( $options.profilesBetaDistribution ) == "True"
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214 --profiles-beta-distribution
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215 #end if
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216 #if str( $options.profilesIntersample ) == "True"
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217 --profiles-intersample
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218 #end if
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219 #if str( $options.profilesDeviationPlots ) == "True"
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220 --profiles-deviation-plots
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221 #end if
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222 #if str( $options.profilesColumns ) != ""
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223 --profiles-columns="$options.profilesColumns"
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224 #end if
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225 #if str( $options.profilesClustering ) == "True"
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226 --profiles-clustering
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227 #end if
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228 #if str( $options.profilesClusteringTopProbes ) != ""
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229 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes"
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230 #end if
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231 #if str( $options.regionProfilesTypes ) != ""
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232 --region-profiles-types="$options.regionProfilesTypes"
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233 #end if
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234 #if str( $options.differential ) == "True"
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235 --differential
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236 #end if
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237 #if str( $options.differentialPermutations ) != ""
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238 --differential-permutations="$options.differentialPermutations"
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239 #end if
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240 #if str( $options.differentialComparisonColumns ) != ""
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241 --differential-comparison-columns="$options.differentialComparisonColumns"
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242 #end if
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243 #if str( $options.differentialEnrichment ) == "True"
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244 --differential-enrichment
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245 #end if
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246 #if str( $options.exportToUcsc ) != ""
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247 --export-to-ucsc="$options.exportToUcsc"
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248 #end if
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249 #if str( $options.exportToBed ) == "True"
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250 --export-to-bed
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251 #end if
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252 #if str( $options.exportToCsv ) == "True"
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253 --export-to-csv
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254 #end if
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255 #if str( $options.exportTypes ) != ""
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256 --export-types="$options.exportTypes"
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257 #end if
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258 #if str( $options.colors3Gradient ) != ""
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259 --colors-3-gradient="$options.colors3Gradient"
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260 #end if
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261 #if str( $options.loggingMemory ) == "True"
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262 --logging-memory
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263 #end if
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264 #if str( $options.usePstoimg ) == "True"
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265 --use-pstoimg
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266 #end if
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267 #end if
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268 </command>
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269 <inputs>
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270 <conditional name="inputDataSelector">
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271 <param name="dataType" type="select" label="Data Type">
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272 <option value="tables">Tabular data</option>
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273 <option value="idats">IDAT files</option>
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274 <option value="gsreport">GenomeStudio report</option>
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275 <option value="geo">Gene Expression Omnibus series</option>
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276 <option value="bed">BED files</option>
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277 </param>
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278 <when value="tables">
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279 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
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280 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
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281 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
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282 </when>
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283 <when value="idats">
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284 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
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285 <conditional name="idatSelector">
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286 <param name="idatSource" type="select" label="IDAT source">
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287 <option value="history">Select from history</option>
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288 <option value="repo">Repository on the server</option>
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289 </param>
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290 <when value="repo">
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291 <param name="idatRepo" type="select" label="Select an IDAT repository">
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292 <options from_data_table="rnbeads_repos">
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293 <filter type="sort_by" column="2" />
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294 <validator type="no_options" message="No repositories are available" />
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295 </options>
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296 </param>
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297 </when>
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298 <when value="history">
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299 <repeat min="1" name="idatSeries" title="Input IDAT file">
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300 <param name="idatFile" type="data" format="idat" label="IDAT file"/>
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301 </repeat>
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302 </when>
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303 </conditional>
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304 </when>
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305 <when value="gsreport">
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306 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
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307 </when>
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308 <when value="geo">
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309 <param name="geoSeries" type="text" label="GEO series" />
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310 </when>
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311 <when value="bed">
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312 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
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313 <repeat min="1" name="bedSeries" title="Input BED file">
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314 <param name="bedFile" type="data" format="bed" label="BED file"/>
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315 </repeat>
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316 </when>
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317 </conditional>
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318 <conditional name="options">
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319 <param name="optionSet" type="select" label="Options Set">
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320 <option value="default">Default options</option>
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321 <option value="full">Full option set</option>
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322 </param>
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323 <when value="default" />
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324 <when value="full">
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325 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
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326 <param name="logging" type="select" label="logging, logical" value="1">
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327 <option value="True">True</option>
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328 <option value="False">False</option>
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329 </param>
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330 <param name="email" type="text" label="email, character" value=""/>
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331 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
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332 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
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333 <option value="True">True</option>
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334 <option value="False">False</option>
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335 </param>
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336 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
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337 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
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338 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
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339 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
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340 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
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341 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
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342 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
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343 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
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344 <option value="True">True</option>
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345 <option value="False">False</option>
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346 </param>
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347 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
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348 <option value="True">True</option>
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349 <option value="False">False</option>
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350 </param>
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351 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
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352 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
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353 <option value="True">True</option>
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354 <option value="False">False</option>
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355 </param>
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356 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
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357 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/>
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358 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
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359 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
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360 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
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361 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/>
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362 <param name="normalizationSubtractBackground" type="select" label="normalization.subtract.background, logical" value="0">
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363 <option value="True">True</option>
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364 <option value="False">False</option>
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365 </param>
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366 <param name="qc" type="select" label="qc, logical" value="1">
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367 <option value="True">True</option>
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368 <option value="False">False</option>
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369 </param>
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370 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
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371 <option value="True">True</option>
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372 <option value="False">False</option>
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373 </param>
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374 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
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375 <option value="True">True</option>
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376 <option value="False">False</option>
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377 </param>
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378 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
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379 <option value="True">True</option>
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380 <option value="False">False</option>
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381 </param>
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382 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
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383 <option value="True">True</option>
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384 <option value="False">False</option>
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385 </param>
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386 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
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387 <option value="True">True</option>
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388 <option value="False">False</option>
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389 </param>
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390 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
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391 <option value="True">True</option>
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392 <option value="False">False</option>
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393 </param>
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394 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/>
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395 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
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396 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
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397 <option value="True">True</option>
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398 <option value="False">False</option>
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399 </param>
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400 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
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401 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
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402 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
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403 <option value="True">True</option>
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404 <option value="False">False</option>
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405 </param>
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406 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
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407 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
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408 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
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409 <option value="True">True</option>
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410 <option value="False">False</option>
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411 </param>
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412 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
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413 <option value="True">True</option>
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414 <option value="False">False</option>
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415 </param>
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416 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
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417 <option value="True">True</option>
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418 <option value="False">False</option>
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419 </param>
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420 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
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421 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
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422 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
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423 <param name="batch" type="select" label="batch, logical" value="1">
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424 <option value="True">True</option>
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425 <option value="False">False</option>
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426 </param>
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427 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
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428 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
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429 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
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430 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
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431 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
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432 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
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|
433 <option value="True">True</option>
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|
434 <option value="False">False</option>
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|
|
435 </param>
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|
436 <param name="profiles" type="select" label="profiles, logical" value="1">
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437 <option value="True">True</option>
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|
438 <option value="False">False</option>
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|
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439 </param>
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|
440 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
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441 <option value="True">True</option>
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|
442 <option value="False">False</option>
|
|
|
443 </param>
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444 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
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445 <option value="True">True</option>
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446 <option value="False">False</option>
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|
|
447 </param>
|
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|
448 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
|
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449 <option value="True">True</option>
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|
450 <option value="False">False</option>
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|
|
451 </param>
|
|
|
452 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
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|
|
453 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
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|
|
454 <option value="True">True</option>
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|
455 <option value="False">False</option>
|
|
|
456 </param>
|
|
|
457 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
|
|
|
458 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
|
|
|
459 <param name="differential" type="select" label="differential, logical" value="1">
|
|
|
460 <option value="True">True</option>
|
|
|
461 <option value="False">False</option>
|
|
|
462 </param>
|
|
|
463 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
|
|
|
464 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
|
|
|
465 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
|
|
|
466 <option value="True">True</option>
|
|
|
467 <option value="False">False</option>
|
|
|
468 </param>
|
|
|
469 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
|
|
|
470 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
|
|
|
471 <option value="True">True</option>
|
|
|
472 <option value="False">False</option>
|
|
|
473 </param>
|
|
|
474 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
|
|
|
475 <option value="True">True</option>
|
|
|
476 <option value="False">False</option>
|
|
|
477 </param>
|
|
|
478 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
|
|
|
479 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
|
|
|
480 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
|
|
|
481 <option value="True">True</option>
|
|
|
482 <option value="False">False</option>
|
|
|
483 </param>
|
|
|
484 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
|
|
|
485 <option value="True">True</option>
|
|
|
486 <option value="False">False</option>
|
|
|
487 </param>
|
|
|
488 </when>
|
|
|
489 </conditional>
|
|
|
490 </inputs>
|
|
|
491
|
|
|
492 <outputs>
|
|
|
493 <data format="html" name="html_file" label="index.html" />
|
|
|
494 </outputs>
|
|
|
495
|
|
|
496 <!--
|
|
|
497 <tests>
|
|
|
498 <test>
|
|
|
499 <param name="input" value="fa_gc_content_input.fa"/>
|
|
|
500 <output name="out_file1" file="fa_gc_content_output.txt"/>
|
|
|
501 </test>
|
|
|
502 </tests> -->
|
|
|
503
|
|
|
504 <help>
|
|
|
505 RnBeads is an R-package for comprehensive analysis of Illumina Infinium HumanMethylation450 BeadChip data. It extends previous approaches for this type of data analysis by high throughput capabilities, as well as presenting results in a comprehensive, highly interpretable fashion.
|
|
|
506 </help>
|
|
|
507
|
|
|
508 </tool> |
