annotate rnbeads.xml @ 33:4feb5eba202c draft

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author pavlo-lutsik
date Fri, 05 Jul 2013 08:21:24 -0400
parents aad84663f9c2
children
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31
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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( $options.columnsPairing ) != ""
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70 --columns-pairing="$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( $options.identifiersColumn ) != ""
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79 --identifiers-column="$options.identifiersColumn"
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80 #end if
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81 #if str( $options.pointsCategory ) != ""
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82 --points-category="$options.pointsCategory"
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83 #end if
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84 #if str( $options.colorsCategory ) != ""
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85 --colors-category="$options.colorsCategory"
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86 #end if
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87 #if str( $options.colorsGradient ) != ""
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88 --colors-gradient="$options.colorsGradient"
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89 #end if
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90 #if str( $options.minGroupSize ) != ""
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91 --min-group-size="$options.minGroupSize"
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92 #end if
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93 #if str( $options.maxGroupCount ) != ""
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94 --max-group-count="$options.maxGroupCount"
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95 #end if
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96 #if str( $options.gzLargeFiles ) == "True"
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97 --gz-large-files
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98 #end if
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99 #if str( $options.strandSpecific ) == "True"
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100 --strand-specific
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101 #end if
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102 #if str( $options.replicateIdColumn ) != ""
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103 --replicate-id-column="$options.replicateIdColumn"
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104 #end if
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105 #if str( $options.loadingNormalization ) == "True"
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106 --loading-normalization
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107 #end if
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108 #if str( $options.loadingDefaultDataType ) != ""
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109 --loading-default-data-type="$options.loadingDefaultDataType"
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110 #end if
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111 #if str( $options.loadingTableSeparator ) != ""
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112 --loading-table-separator="$options.loadingTableSeparator"
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113 #end if
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114 #if str( $options.loadingBedStyle ) != ""
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115 --loading-bed-style="$options.loadingBedStyle"
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116 #end if
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117 #if str( $options.loadingBedColumns ) != ""
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118 --loading-bed-columns="$options.loadingBedColumns"
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119 #end if
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120 #if str( $options.loadingBedFrameShift ) != ""
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121 --loading-bed-frame-shift="$options.loadingBedFrameShift"
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122 #end if
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123 #if str( $options.normalizationMethod ) != ""
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124 --normalization-method="$options.normalizationMethod"
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125 #end if
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126 #if str( $options.normalizationBackgroundMethod ) != ""
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127 --normalization-background-method="$options.normalizationBackgroundMethod"
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128 #end if
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129 #if str( $options.qc ) == "True"
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130 --qc
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131 #end if
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132 #if str( $options.qcBoxplots ) == "True"
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133 --qc-boxplots
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134 #end if
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135 #if str( $options.qcBarplots ) == "True"
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136 --qc-barplots
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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.qcSnpHeatmap ) == "True"
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142 --qc-snp-heatmap
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143 #end if
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144 #if str( $options.qcSnpBoxplot ) == "True"
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145 --qc-snp-boxplot
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146 #end if
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147 #if str( $options.qcSnpBarplot ) == "True"
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148 --qc-snp-barplot
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149 #end if
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150 #if str( $options.qcSampleBatchSize ) != ""
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151 --qc-sample-batch-size="$options.qcSampleBatchSize"
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152 #end if
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153 #if str( $options.filteringContextRemoval ) != ""
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154 --filtering-context-removal="$options.filteringContextRemoval"
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155 #end if
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156 #if str( $options.filteringSnp ) == "True"
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157 --filtering-snp
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158 #end if
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159 #if str( $options.filteringSnpFrequency ) != ""
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160 --filtering-snp-frequency="$options.filteringSnpFrequency"
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161 #end if
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162 #if str( $options.filteringSnpAccepted ) != ""
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163 --filtering-snp-accepted="$options.filteringSnpAccepted"
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164 #end if
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165 #if str( $options.filteringSexChromosomesRemoval ) == "True"
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166 --filtering-sex-chromosomes-removal
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167 #end if
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168 #if str( $options.filteringMissingValueQuantile ) != ""
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169 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
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170 #end if
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171 #if str( $options.filteringCoverageThreshold ) != ""
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172 --filtering-coverage-threshold="$options.filteringCoverageThreshold"
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173 #end if
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174 #if str( $options.filteringLowCoverageMasking ) == "True"
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175 --filtering-low-coverage-masking
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176 #end if
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177 #if str( $options.filteringHighCoverageOutliers ) == "True"
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178 --filtering-high-coverage-outliers
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179 #end if
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180 #if str( $options.filteringGreedycut ) == "True"
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181 --filtering-greedycut
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182 #end if
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183 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
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parents:
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184 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
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pavlo-lutsik
parents:
diff changeset
185 #end if
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pavlo-lutsik
parents:
diff changeset
186 #if str( $options.filteringGreedycutRcTies ) != ""
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
187 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
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pavlo-lutsik
parents:
diff changeset
188 #end if
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pavlo-lutsik
parents:
diff changeset
189 #if str( $options.filteringDeviationThreshold ) != ""
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pavlo-lutsik
parents:
diff changeset
190 --filtering-deviation-threshold="$options.filteringDeviationThreshold"
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pavlo-lutsik
parents:
diff changeset
191 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
192 #if str( $options.batch ) == "True"
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pavlo-lutsik
parents:
diff changeset
193 --batch
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pavlo-lutsik
parents:
diff changeset
194 #end if
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pavlo-lutsik
parents:
diff changeset
195 #if str( $options.batchDreductionColumns ) != ""
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pavlo-lutsik
parents:
diff changeset
196 --batch-dreduction-columns="$options.batchDreductionColumns"
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pavlo-lutsik
parents:
diff changeset
197 #end if
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pavlo-lutsik
parents:
diff changeset
198 #if str( $options.batchPrincipalComponents ) != ""
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pavlo-lutsik
parents:
diff changeset
199 --batch-principal-components="$options.batchPrincipalComponents"
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pavlo-lutsik
parents:
diff changeset
200 #end if
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pavlo-lutsik
parents:
diff changeset
201 #if str( $options.batchCorrelationColumns ) != ""
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pavlo-lutsik
parents:
diff changeset
202 --batch-correlation-columns="$options.batchCorrelationColumns"
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pavlo-lutsik
parents:
diff changeset
203 #end if
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pavlo-lutsik
parents:
diff changeset
204 #if str( $options.batchCorrelationPvalueThreshold ) != ""
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pavlo-lutsik
parents:
diff changeset
205 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold"
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pavlo-lutsik
parents:
diff changeset
206 #end if
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pavlo-lutsik
parents:
diff changeset
207 #if str( $options.batchCorrelationPermutations ) != ""
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pavlo-lutsik
parents:
diff changeset
208 --batch-correlation-permutations="$options.batchCorrelationPermutations"
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pavlo-lutsik
parents:
diff changeset
209 #end if
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pavlo-lutsik
parents:
diff changeset
210 #if str( $options.batchCorrelationQc ) == "True"
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pavlo-lutsik
parents:
diff changeset
211 --batch-correlation-qc
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pavlo-lutsik
parents:
diff changeset
212 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
213 #if str( $options.profiles ) == "True"
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pavlo-lutsik
parents:
diff changeset
214 --profiles
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pavlo-lutsik
parents:
diff changeset
215 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
216 #if str( $options.profilesBetaDistribution ) == "True"
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pavlo-lutsik
parents:
diff changeset
217 --profiles-beta-distribution
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pavlo-lutsik
parents:
diff changeset
218 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
219 #if str( $options.profilesIntersample ) == "True"
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pavlo-lutsik
parents:
diff changeset
220 --profiles-intersample
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pavlo-lutsik
parents:
diff changeset
221 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
222 #if str( $options.profilesDeviationPlots ) == "True"
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pavlo-lutsik
parents:
diff changeset
223 --profiles-deviation-plots
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pavlo-lutsik
parents:
diff changeset
224 #end if
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pavlo-lutsik
parents:
diff changeset
225 #if str( $options.profilesColumns ) != ""
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pavlo-lutsik
parents:
diff changeset
226 --profiles-columns="$options.profilesColumns"
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pavlo-lutsik
parents:
diff changeset
227 #end if
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pavlo-lutsik
parents:
diff changeset
228 #if str( $options.profilesClustering ) == "True"
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pavlo-lutsik
parents:
diff changeset
229 --profiles-clustering
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pavlo-lutsik
parents:
diff changeset
230 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
231 #if str( $options.profilesClusteringTopProbes ) != ""
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pavlo-lutsik
parents:
diff changeset
232 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes"
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pavlo-lutsik
parents:
diff changeset
233 #end if
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pavlo-lutsik
parents:
diff changeset
234 #if str( $options.regionProfilesTypes ) != ""
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pavlo-lutsik
parents:
diff changeset
235 --region-profiles-types="$options.regionProfilesTypes"
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pavlo-lutsik
parents:
diff changeset
236 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
237 #if str( $options.differential ) == "True"
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pavlo-lutsik
parents:
diff changeset
238 --differential
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
239 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
240 #if str( $options.differentialPermutations ) != ""
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pavlo-lutsik
parents:
diff changeset
241 --differential-permutations="$options.differentialPermutations"
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pavlo-lutsik
parents:
diff changeset
242 #end if
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pavlo-lutsik
parents:
diff changeset
243 #if str( $options.differentialComparisonColumns ) != ""
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
244 --differential-comparison-columns="$options.differentialComparisonColumns"
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pavlo-lutsik
parents:
diff changeset
245 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
246 #if str( $options.differentialComparisonColumnsAllPairwise ) != ""
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
247 --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise"
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
248 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
249 #if str( $options.differentialEnrichment ) == "True"
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pavlo-lutsik
parents:
diff changeset
250 --differential-enrichment
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pavlo-lutsik
parents:
diff changeset
251 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
252 #if str( $options.exportToUcsc ) != ""
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pavlo-lutsik
parents:
diff changeset
253 --export-to-ucsc="$options.exportToUcsc"
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pavlo-lutsik
parents:
diff changeset
254 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
255 #if str( $options.exportToBed ) == "True"
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pavlo-lutsik
parents:
diff changeset
256 --export-to-bed
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pavlo-lutsik
parents:
diff changeset
257 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
258 #if str( $options.exportToCsv ) == "True"
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
259 --export-to-csv
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pavlo-lutsik
parents:
diff changeset
260 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
261 #if str( $options.exportTypes ) != ""
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pavlo-lutsik
parents:
diff changeset
262 --export-types="$options.exportTypes"
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pavlo-lutsik
parents:
diff changeset
263 #end if
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pavlo-lutsik
parents:
diff changeset
264 #if str( $options.colors3Gradient ) != ""
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pavlo-lutsik
parents:
diff changeset
265 --colors-3-gradient="$options.colors3Gradient"
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pavlo-lutsik
parents:
diff changeset
266 #end if
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
267 #if str( $options.loggingMemory ) == "True"
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pavlo-lutsik
parents:
diff changeset
268 --logging-memory
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pavlo-lutsik
parents:
diff changeset
269 #end if
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pavlo-lutsik
parents:
diff changeset
270 #end if
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pavlo-lutsik
parents:
diff changeset
271 </command>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
272 <inputs>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
273 <conditional name="inputDataSelector">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
274 <param name="dataType" type="select" label="Data Type">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
275 <option value="tables">Tabular data</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
276 <option value="idats">IDAT files</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
277 <option value="gsreport">GenomeStudio report</option>
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pavlo-lutsik
parents:
diff changeset
278 <option value="geo">Gene Expression Omnibus series</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
279 <option value="bed">BED files</option>
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pavlo-lutsik
parents:
diff changeset
280 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
281 <when value="tables">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
282 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
283 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
284 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
285 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
286 <when value="idats">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
287 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
288 <conditional name="idatSelector">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
289 <param name="idatSource" type="select" label="IDAT source">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
290 <option value="history">Select from history</option>
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pavlo-lutsik
parents:
diff changeset
291 <option value="repo">Repository on the server</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
292 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
293 <when value="repo">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
294 <param name="idatRepo" type="select" label="Select an IDAT repository">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
295 <options from_data_table="rnbeads_repos">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
296 <filter type="sort_by" column="2" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
297 <validator type="no_options" message="No repositories are available" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
298 </options>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
299 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
300 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
301 <when value="history">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
302 <repeat min="1" name="idatSeries" title="Input IDAT file">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
303 <param name="idatFile" type="data" format="idat" label="IDAT file"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
304 </repeat>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
305 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
306 </conditional>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
307 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
308 <when value="gsreport">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
309 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
310 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
311 <when value="geo">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
312 <param name="geoSeries" type="text" label="GEO series" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
313 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
314 <when value="bed">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
315 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
316 <repeat min="1" name="bedSeries" title="Input BED file">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
317 <param name="bedFile" type="data" format="bed" label="BED file"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
318 </repeat>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
319 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
320 </conditional>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
321 <conditional name="options">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
322 <param name="optionSet" type="select" label="Options Set">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
323 <option value="default">Default options</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
324 <option value="full">Full option set</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
325 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
326 <when value="default" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
327 <when value="full">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
328 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
329 <param name="logging" type="select" label="logging, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
330 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
331 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
332 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
333 <param name="email" type="text" label="email, character" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
334 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
335 <param name="columnsPairing" type="text" label="columns.pairing, integer vector" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
336 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
337 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
338 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
339 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
340 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
341 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
342 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
343 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
344 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
345 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
346 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
347 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
348 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
349 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
350 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
351 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
352 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
353 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
354 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
355 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
356 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
357 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
358 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
359 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
360 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
361 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
362 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
363 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
364 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
365 <param name="normalizationMethod" type="text" label="normalization.method, character" value="swan"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
366 <param name="normalizationBackgroundMethod" type="text" label="normalization.background.method, character" value="methylumi.noob"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
367 <param name="qc" type="select" label="qc, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
368 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
369 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
370 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
371 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
372 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
373 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
374 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
375 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
376 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
377 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
378 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
379 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
380 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
381 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
382 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
383 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
384 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
385 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
386 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
387 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
388 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
389 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
390 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
391 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
392 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
393 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
394 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
395 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="500"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
396 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
397 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
398 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
399 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
400 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
401 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
402 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
403 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
404 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
405 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
406 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
407 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
408 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
409 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
410 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
411 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
412 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
413 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
414 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
415 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
416 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
417 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
418 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
419 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
420 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
421 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
422 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
423 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
424 <param name="batch" type="select" label="batch, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
425 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
426 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
427 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
428 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
429 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
430 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
431 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
432 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
433 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
434 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
435 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
436 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
437 <param name="profiles" type="select" label="profiles, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
438 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
439 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
440 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
441 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
442 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
443 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
444 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
445 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
446 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
447 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
448 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
449 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
450 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
451 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
452 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
453 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
454 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
455 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
456 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
457 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
458 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
459 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
460 <param name="differential" type="select" label="differential, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
461 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
462 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
463 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
464 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
465 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
466 <param name="differentialComparisonColumnsAllPairwise" type="text" label="differential.comparison.columns.all.pairwise, integer vector" value=""/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
467 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
468 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
469 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
470 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
471 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
472 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
473 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
474 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
475 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
476 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
477 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
478 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
479 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
480 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
481 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
482 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
483 <option value="True">True</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
484 <option value="False">False</option>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
485 </param>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
486 </when>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
487 </conditional>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
488 </inputs>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
489
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
490 <outputs>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
491 <data format="html" name="html_file" label="index.html" />
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
492 </outputs>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
493
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
494 <!--
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
495 <tests>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
496 <test>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
497 <param name="input" value="fa_gc_content_input.fa"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
498 <output name="out_file1" file="fa_gc_content_output.txt"/>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
499 </test>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
500 </tests> -->
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
501
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
502 <help>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
503 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.
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
504 </help>
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
505
aad84663f9c2 Uploaded
pavlo-lutsik
parents:
diff changeset
506 </tool>