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1 <?xml version="0.9"?>
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2 <tool id="rnbeads" name="RnBeads" version="0.91">
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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="3.1.0">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( $options.columnsPairing ) != ""
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70 --columns-pairing="$options.columnsPairing"
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71 #end if
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72 #if str( $options.analyzeSites ) == "True"
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73 --analyze-sites
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74 #end if
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75 #if str( $options.regionTypes ) != ""
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76 --region-types="$options.regionTypes"
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77 #end if
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78 #if str( $options.regionAggregation ) != ""
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79 --region-aggregation="$options.regionAggregation"
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80 #end if
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81 #if str( $options.regionSubsegments ) != ""
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82 --region-subsegments="$options.regionSubsegments"
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83 #end if
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84 #if str( $options.regionSubsegmentsTypes ) != ""
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85 --region-subsegments-types="$options.regionSubsegmentsTypes"
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86 #end if
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87 #if str( $options.identifiersColumn ) != ""
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88 --identifiers-column="$options.identifiersColumn"
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89 #end if
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90 #if str( $options.pointsCategory ) != ""
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91 --points-category="$options.pointsCategory"
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92 #end if
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93 #if str( $options.colorsCategory ) != ""
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94 --colors-category="$options.colorsCategory"
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95 #end if
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96 #if str( $options.colorsGradient ) != ""
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97 --colors-gradient="$options.colorsGradient"
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98 #end if
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99 #if str( $options.minGroupSize ) != ""
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100 --min-group-size="$options.minGroupSize"
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101 #end if
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102 #if str( $options.maxGroupCount ) != ""
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103 --max-group-count="$options.maxGroupCount"
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104 #end if
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105 #if str( $options.gzLargeFiles ) == "True"
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106 --gz-large-files
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107 #end if
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108 #if str( $options.strandSpecific ) == "True"
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109 --strand-specific
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110 #end if
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111 #if str( $options.replicateIdColumn ) != ""
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112 --replicate-id-column="$options.replicateIdColumn"
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113 #end if
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114 #if str( $options.import ) == "True"
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115 --import
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116 #end if
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117 #if str( $options.importDefaultDataType ) != ""
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118 --import-default-data-type="$options.importDefaultDataType"
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119 #end if
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120 #if str( $options.importTableSeparator ) != ""
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121 --import-table-separator="$options.importTableSeparator"
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122 #end if
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123 #if str( $options.importBedStyle ) != ""
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124 --import-bed-style="$options.importBedStyle"
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125 #end if
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126 #if str( $options.importBedColumns ) != ""
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127 --import-bed-columns="$options.importBedColumns"
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128 #end if
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129 #if str( $options.importBedFrameShift ) != ""
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130 --import-bed-frame-shift="$options.importBedFrameShift"
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131 #end if
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132 #if str( $options.importBedTest ) == "True"
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133 --import-bed-test
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134 #end if
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135 #if str( $options.importBedTestOnly ) == "True"
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136 --import-bed-test-only
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137 #end if
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138 #if str( $options.importIdatChunkSize ) != ""
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139 --import-idat-chunk-size="$options.importIdatChunkSize"
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140 #end if
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141 #if str( $options.preprocessing ) == "True"
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142 --preprocessing
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143 #end if
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144 #if str( $options.qc ) == "True"
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145 --qc
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146 #end if
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147 #if str( $options.qcBoxplots ) == "True"
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148 --qc-boxplots
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149 #end if
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150 #if str( $options.qcBarplots ) == "True"
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151 --qc-barplots
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152 #end if
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153 #if str( $options.qcNegativeBoxplot ) == "True"
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154 --qc-negative-boxplot
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155 #end if
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156 #if str( $options.qcSnpHeatmap ) == "True"
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157 --qc-snp-heatmap
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158 #end if
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159 #if str( $options.qcSnpDistances ) == "True"
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160 --qc-snp-distances
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161 #end if
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162 #if str( $options.qcSnpBoxplot ) == "True"
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163 --qc-snp-boxplot
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164 #end if
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165 #if str( $options.qcSnpBarplot ) == "True"
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166 --qc-snp-barplot
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167 #end if
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168 #if str( $options.qcCoveragePlots ) == "True"
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169 --qc-coverage-plots
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170 #end if
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171 #if str( $options.qcCoverageThresholdPlot ) != ""
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172 --qc-coverage-threshold-plot="$options.qcCoverageThresholdPlot"
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173 #end if
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174 #if str( $options.qcCoverageHistograms ) == "True"
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175 --qc-coverage-histograms
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176 #end if
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177 #if str( $options.qcCoverageViolins ) == "True"
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178 --qc-coverage-violins
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179 #end if
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180 #if str( $options.qcSampleBatchSize ) != ""
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181 --qc-sample-batch-size="$options.qcSampleBatchSize"
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182 #end if
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183 #if str( $options.normalization ) == "True"
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184 --normalization
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185 #end if
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186 #if str( $options.normalizationMethod ) != ""
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187 --normalization-method="$options.normalizationMethod"
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188 #end if
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189 #if str( $options.normalizationBackgroundMethod ) != ""
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190 --normalization-background-method="$options.normalizationBackgroundMethod"
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191 #end if
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192 #if str( $options.normalizationPlotShifts ) == "True"
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193 --normalization-plot-shifts
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194 #end if
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195 #if str( $options.filteringWhitelist ) != ""
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196 --filtering-whitelist="$options.filteringWhitelist"
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197 #end if
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198 #if str( $options.filteringBlacklist ) != ""
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199 --filtering-blacklist="$options.filteringBlacklist"
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200 #end if
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201 #if str( $options.filteringContextRemoval ) != ""
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202 --filtering-context-removal="$options.filteringContextRemoval"
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203 #end if
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204 #if str( $options.filteringSnp ) != ""
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205 --filtering-snp="$options.filteringSnp"
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206 #end if
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207 #if str( $options.filteringSexChromosomesRemoval ) == "True"
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208 --filtering-sex-chromosomes-removal
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209 #end if
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210 #if str( $options.filteringMissingValueQuantile ) != ""
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211 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
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212 #end if
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213 #if str( $options.filteringCoverageThreshold ) != ""
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214 --filtering-coverage-threshold="$options.filteringCoverageThreshold"
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215 #end if
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216 #if str( $options.filteringLowCoverageMasking ) == "True"
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217 --filtering-low-coverage-masking
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218 #end if
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219 #if str( $options.filteringHighCoverageOutliers ) == "True"
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220 --filtering-high-coverage-outliers
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221 #end if
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222 #if str( $options.filteringGreedycut ) == "True"
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223 --filtering-greedycut
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224 #end if
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225 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
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226 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
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227 #end if
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228 #if str( $options.filteringGreedycutRcTies ) != ""
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229 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
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230 #end if
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231 #if str( $options.filteringDeviationThreshold ) != ""
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232 --filtering-deviation-threshold="$options.filteringDeviationThreshold"
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233 #end if
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234 #if str( $options.inference ) == "True"
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235 --inference
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236 #end if
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237 #if str( $options.inferenceTargetsSva ) != ""
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238 --inference-targets-sva="$options.inferenceTargetsSva"
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239 #end if
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240 #if str( $options.inferenceReferenceMethylomeColumn ) != ""
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241 --inference-reference-methylome-column="$options.inferenceReferenceMethylomeColumn"
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242 #end if
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243 #if str( $options.inferenceMaxCellTypeMarkers ) != ""
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244 --inference-max-cell-type-markers="$options.inferenceMaxCellTypeMarkers"
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245 #end if
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246 #if str( $options.inferenceTopCellTypeMarkers ) != ""
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247 --inference-top-cell-type-markers="$options.inferenceTopCellTypeMarkers"
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248 #end if
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249 #if str( $options.inferenceSvaNumMethod ) != ""
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250 --inference-sva-num-method="$options.inferenceSvaNumMethod"
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251 #end if
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252 #if str( $options.exploratory ) == "True"
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253 --exploratory
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254 #end if
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255 #if str( $options.exploratoryColumns ) != ""
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256 --exploratory-columns="$options.exploratoryColumns"
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257 #end if
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258 #if str( $options.exploratoryTopDimensions ) != ""
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259 --exploratory-top-dimensions="$options.exploratoryTopDimensions"
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260 #end if
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261 #if str( $options.exploratoryPrincipalComponents ) != ""
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262 --exploratory-principal-components="$options.exploratoryPrincipalComponents"
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263 #end if
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264 #if str( $options.exploratoryCorrelationPvalueThreshold ) != ""
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265 --exploratory-correlation-pvalue-threshold="$options.exploratoryCorrelationPvalueThreshold"
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266 #end if
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267 #if str( $options.exploratoryCorrelationPermutations ) != ""
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268 --exploratory-correlation-permutations="$options.exploratoryCorrelationPermutations"
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269 #end if
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270 #if str( $options.exploratoryCorrelationQc ) == "True"
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271 --exploratory-correlation-qc
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272 #end if
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273 #if str( $options.exploratoryBetaDistribution ) == "True"
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274 --exploratory-beta-distribution
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275 #end if
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276 #if str( $options.exploratoryIntersample ) == "True"
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277 --exploratory-intersample
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278 #end if
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279 #if str( $options.exploratoryDeviationPlots ) == "True"
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280 --exploratory-deviation-plots
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281 #end if
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282 #if str( $options.exploratoryClustering ) != ""
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283 --exploratory-clustering="$options.exploratoryClustering"
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284 #end if
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285 #if str( $options.exploratoryClusteringTopSites ) != ""
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286 --exploratory-clustering-top-sites="$options.exploratoryClusteringTopSites"
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287 #end if
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288 #if str( $options.exploratoryRegionProfiles ) != ""
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289 --exploratory-region-profiles="$options.exploratoryRegionProfiles"
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290 #end if
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291 #if str( $options.differential ) == "True"
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292 --differential
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293 #end if
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294 #if str( $options.differentialSiteTestMethod ) != ""
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295 --differential-site-test-method="$options.differentialSiteTestMethod"
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296 #end if
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297 #if str( $options.differentialPermutations ) != ""
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298 --differential-permutations="$options.differentialPermutations"
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299 #end if
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300 #if str( $options.differentialComparisonColumns ) != ""
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301 --differential-comparison-columns="$options.differentialComparisonColumns"
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302 #end if
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303 #if str( $options.differentialComparisonColumnsAllPairwise ) != ""
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304 --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise"
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305 #end if
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306 #if str( $options.covariateAdjustmentColumns ) != ""
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307 --covariate-adjustment-columns="$options.covariateAdjustmentColumns"
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308 #end if
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309 #if str( $options.differentialAdjustmentSva ) == "True"
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310 --differential-adjustment-sva
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311 #end if
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312 #if str( $options.differentialAdjustmentCelltype ) == "True"
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313 --differential-adjustment-celltype
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314 #end if
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315 #if str( $options.differentialEnrichment ) == "True"
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316 --differential-enrichment
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317 #end if
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318 #if str( $options.exportToBed ) == "True"
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319 --export-to-bed
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320 #end if
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321 #if str( $options.exportToTrackhub ) != ""
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322 --export-to-trackhub="$options.exportToTrackhub"
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323 #end if
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324 #if str( $options.exportToCsv ) == "True"
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325 --export-to-csv
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326 #end if
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327 #if str( $options.exportToEwasher ) == "True"
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328 --export-to-ewasher
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329 #end if
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330 #if str( $options.exportTypes ) != ""
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331 --export-types="$options.exportTypes"
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332 #end if
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333 #if str( $options.colorsMeth ) != ""
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334 --colors-meth="$options.colorsMeth"
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335 #end if
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336 #if str( $options.colors3Gradient ) != ""
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337 --colors-3-gradient="$options.colors3Gradient"
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338 #end if
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339 #if str( $options.loggingMemory ) == "True"
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340 --logging-memory
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341 #end if
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342 #if str( $options.loggingDisk ) == "True"
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343 --logging-disk
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344 #end if
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345 #if str( $options.loggingExitOnError ) == "True"
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346 --logging-exit-on-error
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347 #end if
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348 #if str( $options.distributionSubsample ) != ""
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349 --distribution-subsample="$options.distributionSubsample"
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350 #end if
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351 #if str( $options.diskDumpBigMatrices ) == "True"
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352 --disk-dump-big-matrices
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353 #end if
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354 #if str( $options.enforceMemoryManagement ) == "True"
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355 --enforce-memory-management
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356 #end if
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357 #if str( $options.enforceDestroyDiskDumps ) == "True"
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358 --enforce-destroy-disk-dumps
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359 #end if
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360 #end if
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361 </command>
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362 <inputs>
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363 <conditional name="inputDataSelector">
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364 <param name="dataType" type="select" label="Data Type">
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365 <option value="tables">Tabular data</option>
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366 <option value="idats">IDAT files</option>
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367 <option value="gsreport">GenomeStudio report</option>
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368 <option value="geo">Gene Expression Omnibus series</option>
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369 <option value="bed">BED files</option>
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370 </param>
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|
|
371 <when value="tables">
|
|
|
372 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
|
|
|
373 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
|
|
|
374 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
|
|
|
375 </when>
|
|
|
376 <when value="idats">
|
|
|
377 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
|
|
|
378 <conditional name="idatSelector">
|
|
|
379 <param name="idatSource" type="select" label="IDAT source">
|
|
|
380 <option value="history">Select from history</option>
|
|
|
381 <option value="repo">Repository on the server</option>
|
|
|
382 </param>
|
|
|
383 <when value="repo">
|
|
|
384 <param name="idatRepo" type="select" label="Select an IDAT repository">
|
|
|
385 <options from_data_table="rnbeads_repos">
|
|
|
386 <filter type="sort_by" column="2" />
|
|
|
387 <validator type="no_options" message="No repositories are available" />
|
|
|
388 </options>
|
|
|
389 </param>
|
|
|
390 </when>
|
|
|
391 <when value="history">
|
|
|
392 <repeat min="1" name="idatSeries" title="Input IDAT file">
|
|
|
393 <param name="idatFile" type="data" format="idat" label="IDAT file"/>
|
|
|
394 </repeat>
|
|
|
395 </when>
|
|
|
396 </conditional>
|
|
|
397 </when>
|
|
|
398 <when value="gsreport">
|
|
|
399 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
|
|
|
400 </when>
|
|
|
401 <when value="geo">
|
|
|
402 <param name="geoSeries" type="text" label="GEO series" />
|
|
|
403 </when>
|
|
|
404 <when value="bed">
|
|
|
405 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
|
|
|
406 <repeat min="1" name="bedSeries" title="Input BED file">
|
|
|
407 <param name="bedFile" type="data" format="bed" label="BED file"/>
|
|
|
408 </repeat>
|
|
|
409 </when>
|
|
|
410 </conditional>
|
|
|
411 <conditional name="options">
|
|
|
412 <param name="optionSet" type="select" label="Options Set">
|
|
|
413 <option value="default">Default options</option>
|
|
|
414 <option value="full">Full option set</option>
|
|
|
415 </param>
|
|
|
416 <when value="default" />
|
|
|
417 <when value="full">
|
|
|
418 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
|
|
|
419 <param name="logging" type="select" label="logging, logical" value="1">
|
|
|
420 <option value="True">True</option>
|
|
|
421 <option value="False">False</option>
|
|
|
422 </param>
|
|
|
423 <param name="email" type="text" label="email, character" value=""/>
|
|
|
424 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
|
|
|
425 <param name="columnsPairing" type="text" label="columns.pairing, integer vector" value=""/>
|
|
|
426 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
|
|
|
427 <option value="True">True</option>
|
|
|
428 <option value="False">False</option>
|
|
|
429 </param>
|
|
|
430 <param name="regionTypes" type="text" label="region.types, character vector" value=""/>
|
|
|
431 <param name="regionAggregation" type="text" label="region.aggregation, character" value="mean"/>
|
|
|
432 <param name="regionSubsegments" type="text" label="region.subsegments, integer" value="0"/>
|
|
|
433 <param name="regionSubsegmentsTypes" type="text" label="region.subsegments.types, character vector" value=""/>
|
|
|
434 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
|
|
|
435 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
|
|
|
436 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
|
|
|
437 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
|
|
|
438 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
|
|
|
439 <param name="maxGroupCount" type="text" label="max.group.count, integer" value=""/>
|
|
|
440 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
|
|
|
441 <option value="True">True</option>
|
|
|
442 <option value="False">False</option>
|
|
|
443 </param>
|
|
|
444 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
|
|
|
445 <option value="True">True</option>
|
|
|
446 <option value="False">False</option>
|
|
|
447 </param>
|
|
|
448 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
|
|
|
449 <param name="import" type="select" label="import, logical" value="1">
|
|
|
450 <option value="True">True</option>
|
|
|
451 <option value="False">False</option>
|
|
|
452 </param>
|
|
|
453 <param name="importDefaultDataType" type="text" label="import.default.data.type, character" value="idat.dir"/>
|
|
|
454 <param name="importTableSeparator" type="text" label="import.table.separator, character" value=","/>
|
|
|
455 <param name="importBedStyle" type="text" label="import.bed.style, character" value="BisSNP"/>
|
|
|
456 <param name="importBedColumns" type="text" label="import.bed.columns, integer vector" value="1,2,3,6,4,5"/>
|
|
|
457 <param name="importBedFrameShift" type="text" label="import.bed.frame.shift, integer" value="1"/>
|
|
|
458 <param name="importBedTest" type="select" label="import.bed.test, logical" value="1">
|
|
|
459 <option value="True">True</option>
|
|
|
460 <option value="False">False</option>
|
|
|
461 </param>
|
|
|
462 <param name="importBedTestOnly" type="select" label="import.bed.test.only, logical" value="0">
|
|
|
463 <option value="True">True</option>
|
|
|
464 <option value="False">False</option>
|
|
|
465 </param>
|
|
|
466 <param name="importIdatChunkSize" type="text" label="import.idat.chunk.size, integer" value=""/>
|
|
|
467 <param name="preprocessing" type="select" label="preprocessing, logical" value="1">
|
|
|
468 <option value="True">True</option>
|
|
|
469 <option value="False">False</option>
|
|
|
470 </param>
|
|
|
471 <param name="qc" type="select" label="qc, logical" value="1">
|
|
|
472 <option value="True">True</option>
|
|
|
473 <option value="False">False</option>
|
|
|
474 </param>
|
|
|
475 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
|
|
|
476 <option value="True">True</option>
|
|
|
477 <option value="False">False</option>
|
|
|
478 </param>
|
|
|
479 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
|
|
|
480 <option value="True">True</option>
|
|
|
481 <option value="False">False</option>
|
|
|
482 </param>
|
|
|
483 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
|
|
|
484 <option value="True">True</option>
|
|
|
485 <option value="False">False</option>
|
|
|
486 </param>
|
|
|
487 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
|
|
|
488 <option value="True">True</option>
|
|
|
489 <option value="False">False</option>
|
|
|
490 </param>
|
|
|
491 <param name="qcSnpDistances" type="select" label="qc.snp.distances, logical" value="1">
|
|
|
492 <option value="True">True</option>
|
|
|
493 <option value="False">False</option>
|
|
|
494 </param>
|
|
|
495 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
|
|
|
496 <option value="True">True</option>
|
|
|
497 <option value="False">False</option>
|
|
|
498 </param>
|
|
|
499 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
|
|
|
500 <option value="True">True</option>
|
|
|
501 <option value="False">False</option>
|
|
|
502 </param>
|
|
|
503 <param name="qcCoveragePlots" type="select" label="qc.coverage.plots, logical" value="0">
|
|
|
504 <option value="True">True</option>
|
|
|
505 <option value="False">False</option>
|
|
|
506 </param>
|
|
|
507 <param name="qcCoverageThresholdPlot" type="text" label="qc.coverage.threshold.plot, integer vector" value="1,2,3,4,5,6,7,8,9,10"/>
|
|
|
508 <param name="qcCoverageHistograms" type="select" label="qc.coverage.histograms, logical" value="1">
|
|
|
509 <option value="True">True</option>
|
|
|
510 <option value="False">False</option>
|
|
|
511 </param>
|
|
|
512 <param name="qcCoverageViolins" type="select" label="qc.coverage.violins, logical" value="1">
|
|
|
513 <option value="True">True</option>
|
|
|
514 <option value="False">False</option>
|
|
|
515 </param>
|
|
|
516 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="500"/>
|
|
|
517 <param name="normalization" type="select" label="normalization, logical" value="0">
|
|
|
518 <option value="True">True</option>
|
|
|
519 <option value="False">False</option>
|
|
|
520 </param>
|
|
|
521 <param name="normalizationMethod" type="text" label="normalization.method, character" value="swan"/>
|
|
|
522 <param name="normalizationBackgroundMethod" type="text" label="normalization.background.method, character" value="methylumi.noob"/>
|
|
|
523 <param name="normalizationPlotShifts" type="select" label="normalization.plot.shifts, logical" value="1">
|
|
|
524 <option value="True">True</option>
|
|
|
525 <option value="False">False</option>
|
|
|
526 </param>
|
|
|
527 <param name="filteringWhitelist" type="text" label="filtering.whitelist, character" value=""/>
|
|
|
528 <param name="filteringBlacklist" type="text" label="filtering.blacklist, character" value=""/>
|
|
|
529 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
|
|
|
530 <param name="filteringSnp" type="text" label="filtering.snp, character" value="3"/>
|
|
|
531 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
|
|
|
532 <option value="True">True</option>
|
|
|
533 <option value="False">False</option>
|
|
|
534 </param>
|
|
|
535 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
|
|
|
536 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
|
|
|
537 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
|
|
|
538 <option value="True">True</option>
|
|
|
539 <option value="False">False</option>
|
|
|
540 </param>
|
|
|
541 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
|
|
|
542 <option value="True">True</option>
|
|
|
543 <option value="False">False</option>
|
|
|
544 </param>
|
|
|
545 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
|
|
|
546 <option value="True">True</option>
|
|
|
547 <option value="False">False</option>
|
|
|
548 </param>
|
|
|
549 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
|
|
|
550 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
|
|
|
551 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
|
|
|
552 <param name="inference" type="select" label="inference, logical" value="0">
|
|
|
553 <option value="True">True</option>
|
|
|
554 <option value="False">False</option>
|
|
|
555 </param>
|
|
|
556 <param name="inferenceTargetsSva" type="text" label="inference.targets.sva, character vector" value=""/>
|
|
|
557 <param name="inferenceReferenceMethylomeColumn" type="text" label="inference.reference.methylome.column, character" value=""/>
|
|
|
558 <param name="inferenceMaxCellTypeMarkers" type="text" label="inference.max.cell.type.markers, integer" value="10000"/>
|
|
|
559 <param name="inferenceTopCellTypeMarkers" type="text" label="inference.top.cell.type.markers, integer" value="500"/>
|
|
|
560 <param name="inferenceSvaNumMethod" type="text" label="inference.sva.num.method, character" value="leek"/>
|
|
|
561 <param name="exploratory" type="select" label="exploratory, logical" value="1">
|
|
|
562 <option value="True">True</option>
|
|
|
563 <option value="False">False</option>
|
|
|
564 </param>
|
|
|
565 <param name="exploratoryColumns" type="text" label="exploratory.columns, integer vector" value=""/>
|
|
|
566 <param name="exploratoryTopDimensions" type="text" label="exploratory.top.dimensions, integer" value="0"/>
|
|
|
567 <param name="exploratoryPrincipalComponents" type="text" label="exploratory.principal.components, integer" value="8"/>
|
|
|
568 <param name="exploratoryCorrelationPvalueThreshold" type="text" label="exploratory.correlation.pvalue.threshold, double" value="0.01"/>
|
|
|
569 <param name="exploratoryCorrelationPermutations" type="text" label="exploratory.correlation.permutations, integer" value="10000"/>
|
|
|
570 <param name="exploratoryCorrelationQc" type="select" label="exploratory.correlation.qc, logical" value="1">
|
|
|
571 <option value="True">True</option>
|
|
|
572 <option value="False">False</option>
|
|
|
573 </param>
|
|
|
574 <param name="exploratoryBetaDistribution" type="select" label="exploratory.beta.distribution, logical" value="1">
|
|
|
575 <option value="True">True</option>
|
|
|
576 <option value="False">False</option>
|
|
|
577 </param>
|
|
|
578 <param name="exploratoryIntersample" type="select" label="exploratory.intersample, logical" value="1">
|
|
|
579 <option value="True">True</option>
|
|
|
580 <option value="False">False</option>
|
|
|
581 </param>
|
|
|
582 <param name="exploratoryDeviationPlots" type="select" label="exploratory.deviation.plots, logical" value="0">
|
|
|
583 <option value="True">True</option>
|
|
|
584 <option value="False">False</option>
|
|
|
585 </param>
|
|
|
586 <param name="exploratoryClustering" type="text" label="exploratory.clustering, character" value="all"/>
|
|
|
587 <param name="exploratoryClusteringTopSites" type="text" label="exploratory.clustering.top.sites, integer vector" value="1000"/>
|
|
|
588 <param name="exploratoryRegionProfiles" type="text" label="exploratory.region.profiles, character vector" value="genes,promoters,cpgislands"/>
|
|
|
589 <param name="differential" type="select" label="differential, logical" value="1">
|
|
|
590 <option value="True">True</option>
|
|
|
591 <option value="False">False</option>
|
|
|
592 </param>
|
|
|
593 <param name="differentialSiteTestMethod" type="text" label="differential.site.test.method, character" value="limma"/>
|
|
|
594 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
|
|
|
595 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
|
|
|
596 <param name="differentialComparisonColumnsAllPairwise" type="text" label="differential.comparison.columns.all.pairwise, integer vector" value=""/>
|
|
|
597 <param name="covariateAdjustmentColumns" type="text" label="covariate.adjustment.columns, integer vector" value=""/>
|
|
|
598 <param name="differentialAdjustmentSva" type="select" label="differential.adjustment.sva, logical" value="1">
|
|
|
599 <option value="True">True</option>
|
|
|
600 <option value="False">False</option>
|
|
|
601 </param>
|
|
|
602 <param name="differentialAdjustmentCelltype" type="select" label="differential.adjustment.celltype, logical" value="1">
|
|
|
603 <option value="True">True</option>
|
|
|
604 <option value="False">False</option>
|
|
|
605 </param>
|
|
|
606 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
|
|
|
607 <option value="True">True</option>
|
|
|
608 <option value="False">False</option>
|
|
|
609 </param>
|
|
|
610 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
|
|
|
611 <option value="True">True</option>
|
|
|
612 <option value="False">False</option>
|
|
|
613 </param>
|
|
|
614 <param name="exportToTrackhub" type="text" label="export.to.trackhub, character vector" value="bigBed,bigWig"/>
|
|
|
615 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
|
|
|
616 <option value="True">True</option>
|
|
|
617 <option value="False">False</option>
|
|
|
618 </param>
|
|
|
619 <param name="exportToEwasher" type="select" label="export.to.ewasher, logical" value="0">
|
|
|
620 <option value="True">True</option>
|
|
|
621 <option value="False">False</option>
|
|
|
622 </param>
|
|
|
623 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
|
|
|
624 <param name="colorsMeth" type="text" label="colors.meth, character vector" value="#AD0021,#909090,#39278C"/>
|
|
|
625 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
|
|
|
626 <param name="loggingMemory" type="select" label="logging.memory, logical" value="1">
|
|
|
627 <option value="True">True</option>
|
|
|
628 <option value="False">False</option>
|
|
|
629 </param>
|
|
|
630 <param name="loggingDisk" type="select" label="logging.disk, logical" value="0">
|
|
|
631 <option value="True">True</option>
|
|
|
632 <option value="False">False</option>
|
|
|
633 </param>
|
|
|
634 <param name="loggingExitOnError" type="select" label="logging.exit.on.error, logical" value="0">
|
|
|
635 <option value="True">True</option>
|
|
|
636 <option value="False">False</option>
|
|
|
637 </param>
|
|
|
638 <param name="distributionSubsample" type="text" label="distribution.subsample, integer" value="1000000"/>
|
|
|
639 <param name="diskDumpBigMatrices" type="select" label="disk.dump.big.matrices, logical" value="0">
|
|
|
640 <option value="True">True</option>
|
|
|
641 <option value="False">False</option>
|
|
|
642 </param>
|
|
|
643 <param name="enforceMemoryManagement" type="select" label="enforce.memory.management, logical" value="0">
|
|
|
644 <option value="True">True</option>
|
|
|
645 <option value="False">False</option>
|
|
|
646 </param>
|
|
|
647 <param name="enforceDestroyDiskDumps" type="select" label="enforce.destroy.disk.dumps, logical" value="0">
|
|
|
648 <option value="True">True</option>
|
|
|
649 <option value="False">False</option>
|
|
|
650 </param>
|
|
|
651 </when>
|
|
|
652 </conditional>
|
|
|
653 </inputs>
|
|
|
654
|
|
|
655 <outputs>
|
|
|
656 <data format="html" name="html_file" label="index.html" />
|
|
|
657 </outputs>
|
|
|
658
|
|
|
659 <!--
|
|
|
660 <tests>
|
|
|
661 <test>
|
|
|
662 <param name="input" value="fa_gc_content_input.fa"/>
|
|
|
663 <output name="out_file1" file="fa_gc_content_output.txt"/>
|
|
|
664 </test>
|
|
|
665 </tests> -->
|
|
|
666
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667 <help>
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668 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.
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669 </help>
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670
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671 <stdio>
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672 <exit_code range="3:" level="fatal" description="Pipeline error" />
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673 </stdio>
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674
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675 </tool> |
