Mercurial > repos > pavlo-lutsik > rnbeads
comparison rnbeads.xml @ 45:6b0981ab063e draft default tip
Uploaded
| author | pavlo-lutsik |
|---|---|
| date | Thu, 14 Aug 2014 14:56:18 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 44:51c4548d56ed | 45:6b0981ab063e |
|---|---|
| 1 <?xml version="0.9"?> | |
| 2 <tool id="rnbeads" name="RnBeads" version="0.91"> | |
| 3 <description>Performs RnBeads analysis for the selected set of </description> | |
| 4 <requirements> | |
| 5 <requirement type="set_environment" version="1.0">R_SCRIPTS_PATH</requirement> | |
| 6 <requirement type="package" version="3.1.0">R</requirement> | |
| 7 </requirements> | |
| 8 <command interpreter="bash">rnbeads_galaxy_wrapper.sh | |
| 9 --report-dir="$html_file.extra_files_path" | |
| 10 --output-file="$html_file" | |
| 11 #if str( $inputDataSelector.dataType ) == "idats" | |
| 12 --pheno="$inputDataSelector.sampleAnnotations" | |
| 13 #end if | |
| 14 #if str( $inputDataSelector.dataType ) != "idats" | |
| 15 #pass | |
| 16 #else if str( $inputDataSelector.idatSelector.idatSource ) == "history" | |
| 17 --data-type="idatFiles" | |
| 18 #set $idatList="" | |
| 19 #for $input_file in $inputDataSelector.idatSelector.idatSeries: | |
| 20 #set $idatList+=str( $input_file.idatFile ) | |
| 21 #set $idatList+="," | |
| 22 #end for | |
| 23 --idat-files="$idatList" | |
| 24 #else: | |
| 25 --data-type="idatDir" | |
| 26 --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path" | |
| 27 #end if | |
| 28 #if str( $inputDataSelector.dataType ) == "gsreport" | |
| 29 --data-type="GS.report" | |
| 30 --gs-report="$inputDataSelector.gsReportFile" | |
| 31 #end if | |
| 32 #if str( $inputDataSelector.dataType ) == "geo" | |
| 33 --data-type="GEO" | |
| 34 --geo-series=$inputDataSelector.geoSeries | |
| 35 #end if | |
| 36 #if str( $inputDataSelector.dataType ) == "tables" | |
| 37 --data-type="data.files" | |
| 38 --pheno="$inputDataSelector.sampleAnnotations" | |
| 39 #end if | |
| 40 #if str( $inputDataSelector.dataType ) == "tables" | |
| 41 --data-type="data.files" | |
| 42 --pheno="$inputDataSelector.sampleAnnotations" | |
| 43 --betas="$inputDataSelector.betaTable" | |
| 44 --pvals="$inputDataSelector.pvalTable" | |
| 45 #end if | |
| 46 #if str( $inputDataSelector.dataType ) == "bed" | |
| 47 --data-type="bed.dir" | |
| 48 --pheno="$inputDataSelector.sampleAnnotations" | |
| 49 #set $bedList="" | |
| 50 #for $input_file in $inputDataSelector.bedSeries: | |
| 51 #set $bedList+=str( $input_file.bedFile ) | |
| 52 #set $bedList+="," | |
| 53 #end for | |
| 54 --bed-files="$bedList" | |
| 55 #end if | |
| 56 #if str( $options.optionSet ) == "full" | |
| 57 #if str( $options.analysisName ) != "" | |
| 58 --analysis-name="$options.analysisName" | |
| 59 #end if | |
| 60 #if str( $options.logging ) == "True" | |
| 61 --logging | |
| 62 #end if | |
| 63 #if str( $options.email ) != "" | |
| 64 --email="$options.email" | |
| 65 #end if | |
| 66 #if str( $options.assembly ) != "" | |
| 67 --assembly="$options.assembly" | |
| 68 #end if | |
| 69 #if str( $options.columnsPairing ) != "" | |
| 70 --columns-pairing="$options.columnsPairing" | |
| 71 #end if | |
| 72 #if str( $options.analyzeSites ) == "True" | |
| 73 --analyze-sites | |
| 74 #end if | |
| 75 #if str( $options.regionTypes ) != "" | |
| 76 --region-types="$options.regionTypes" | |
| 77 #end if | |
| 78 #if str( $options.regionAggregation ) != "" | |
| 79 --region-aggregation="$options.regionAggregation" | |
| 80 #end if | |
| 81 #if str( $options.regionSubsegments ) != "" | |
| 82 --region-subsegments="$options.regionSubsegments" | |
| 83 #end if | |
| 84 #if str( $options.regionSubsegmentsTypes ) != "" | |
| 85 --region-subsegments-types="$options.regionSubsegmentsTypes" | |
| 86 #end if | |
| 87 #if str( $options.identifiersColumn ) != "" | |
| 88 --identifiers-column="$options.identifiersColumn" | |
| 89 #end if | |
| 90 #if str( $options.pointsCategory ) != "" | |
| 91 --points-category="$options.pointsCategory" | |
| 92 #end if | |
| 93 #if str( $options.colorsCategory ) != "" | |
| 94 --colors-category="$options.colorsCategory" | |
| 95 #end if | |
| 96 #if str( $options.colorsGradient ) != "" | |
| 97 --colors-gradient="$options.colorsGradient" | |
| 98 #end if | |
| 99 #if str( $options.minGroupSize ) != "" | |
| 100 --min-group-size="$options.minGroupSize" | |
| 101 #end if | |
| 102 #if str( $options.maxGroupCount ) != "" | |
| 103 --max-group-count="$options.maxGroupCount" | |
| 104 #end if | |
| 105 #if str( $options.gzLargeFiles ) == "True" | |
| 106 --gz-large-files | |
| 107 #end if | |
| 108 #if str( $options.strandSpecific ) == "True" | |
| 109 --strand-specific | |
| 110 #end if | |
| 111 #if str( $options.replicateIdColumn ) != "" | |
| 112 --replicate-id-column="$options.replicateIdColumn" | |
| 113 #end if | |
| 114 #if str( $options.import ) == "True" | |
| 115 --import | |
| 116 #end if | |
| 117 #if str( $options.importDefaultDataType ) != "" | |
| 118 --import-default-data-type="$options.importDefaultDataType" | |
| 119 #end if | |
| 120 #if str( $options.importTableSeparator ) != "" | |
| 121 --import-table-separator="$options.importTableSeparator" | |
| 122 #end if | |
| 123 #if str( $options.importBedStyle ) != "" | |
| 124 --import-bed-style="$options.importBedStyle" | |
| 125 #end if | |
| 126 #if str( $options.importBedColumns ) != "" | |
| 127 --import-bed-columns="$options.importBedColumns" | |
| 128 #end if | |
| 129 #if str( $options.importBedFrameShift ) != "" | |
| 130 --import-bed-frame-shift="$options.importBedFrameShift" | |
| 131 #end if | |
| 132 #if str( $options.importBedTest ) == "True" | |
| 133 --import-bed-test | |
| 134 #end if | |
| 135 #if str( $options.importBedTestOnly ) == "True" | |
| 136 --import-bed-test-only | |
| 137 #end if | |
| 138 #if str( $options.importIdatChunkSize ) != "" | |
| 139 --import-idat-chunk-size="$options.importIdatChunkSize" | |
| 140 #end if | |
| 141 #if str( $options.preprocessing ) == "True" | |
| 142 --preprocessing | |
| 143 #end if | |
| 144 #if str( $options.qc ) == "True" | |
| 145 --qc | |
| 146 #end if | |
| 147 #if str( $options.qcBoxplots ) == "True" | |
| 148 --qc-boxplots | |
| 149 #end if | |
| 150 #if str( $options.qcBarplots ) == "True" | |
| 151 --qc-barplots | |
| 152 #end if | |
| 153 #if str( $options.qcNegativeBoxplot ) == "True" | |
| 154 --qc-negative-boxplot | |
| 155 #end if | |
| 156 #if str( $options.qcSnpHeatmap ) == "True" | |
| 157 --qc-snp-heatmap | |
| 158 #end if | |
| 159 #if str( $options.qcSnpDistances ) == "True" | |
| 160 --qc-snp-distances | |
| 161 #end if | |
| 162 #if str( $options.qcSnpBoxplot ) == "True" | |
| 163 --qc-snp-boxplot | |
| 164 #end if | |
| 165 #if str( $options.qcSnpBarplot ) == "True" | |
| 166 --qc-snp-barplot | |
| 167 #end if | |
| 168 #if str( $options.qcCoveragePlots ) == "True" | |
| 169 --qc-coverage-plots | |
| 170 #end if | |
| 171 #if str( $options.qcCoverageThresholdPlot ) != "" | |
| 172 --qc-coverage-threshold-plot="$options.qcCoverageThresholdPlot" | |
| 173 #end if | |
| 174 #if str( $options.qcCoverageHistograms ) == "True" | |
| 175 --qc-coverage-histograms | |
| 176 #end if | |
| 177 #if str( $options.qcCoverageViolins ) == "True" | |
| 178 --qc-coverage-violins | |
| 179 #end if | |
| 180 #if str( $options.qcSampleBatchSize ) != "" | |
| 181 --qc-sample-batch-size="$options.qcSampleBatchSize" | |
| 182 #end if | |
| 183 #if str( $options.normalization ) == "True" | |
| 184 --normalization | |
| 185 #end if | |
| 186 #if str( $options.normalizationMethod ) != "" | |
| 187 --normalization-method="$options.normalizationMethod" | |
| 188 #end if | |
| 189 #if str( $options.normalizationBackgroundMethod ) != "" | |
| 190 --normalization-background-method="$options.normalizationBackgroundMethod" | |
| 191 #end if | |
| 192 #if str( $options.normalizationPlotShifts ) == "True" | |
| 193 --normalization-plot-shifts | |
| 194 #end if | |
| 195 #if str( $options.filteringWhitelist ) != "" | |
| 196 --filtering-whitelist="$options.filteringWhitelist" | |
| 197 #end if | |
| 198 #if str( $options.filteringBlacklist ) != "" | |
| 199 --filtering-blacklist="$options.filteringBlacklist" | |
| 200 #end if | |
| 201 #if str( $options.filteringContextRemoval ) != "" | |
| 202 --filtering-context-removal="$options.filteringContextRemoval" | |
| 203 #end if | |
| 204 #if str( $options.filteringSnp ) != "" | |
| 205 --filtering-snp="$options.filteringSnp" | |
| 206 #end if | |
| 207 #if str( $options.filteringSexChromosomesRemoval ) == "True" | |
| 208 --filtering-sex-chromosomes-removal | |
| 209 #end if | |
| 210 #if str( $options.filteringMissingValueQuantile ) != "" | |
| 211 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile" | |
| 212 #end if | |
| 213 #if str( $options.filteringCoverageThreshold ) != "" | |
| 214 --filtering-coverage-threshold="$options.filteringCoverageThreshold" | |
| 215 #end if | |
| 216 #if str( $options.filteringLowCoverageMasking ) == "True" | |
| 217 --filtering-low-coverage-masking | |
| 218 #end if | |
| 219 #if str( $options.filteringHighCoverageOutliers ) == "True" | |
| 220 --filtering-high-coverage-outliers | |
| 221 #end if | |
| 222 #if str( $options.filteringGreedycut ) == "True" | |
| 223 --filtering-greedycut | |
| 224 #end if | |
| 225 #if str( $options.filteringGreedycutPvalueThreshold ) != "" | |
| 226 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" | |
| 227 #end if | |
| 228 #if str( $options.filteringGreedycutRcTies ) != "" | |
| 229 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" | |
| 230 #end if | |
| 231 #if str( $options.filteringDeviationThreshold ) != "" | |
| 232 --filtering-deviation-threshold="$options.filteringDeviationThreshold" | |
| 233 #end if | |
| 234 #if str( $options.inference ) == "True" | |
| 235 --inference | |
| 236 #end if | |
| 237 #if str( $options.inferenceTargetsSva ) != "" | |
| 238 --inference-targets-sva="$options.inferenceTargetsSva" | |
| 239 #end if | |
| 240 #if str( $options.inferenceReferenceMethylomeColumn ) != "" | |
| 241 --inference-reference-methylome-column="$options.inferenceReferenceMethylomeColumn" | |
| 242 #end if | |
| 243 #if str( $options.inferenceMaxCellTypeMarkers ) != "" | |
| 244 --inference-max-cell-type-markers="$options.inferenceMaxCellTypeMarkers" | |
| 245 #end if | |
| 246 #if str( $options.inferenceTopCellTypeMarkers ) != "" | |
| 247 --inference-top-cell-type-markers="$options.inferenceTopCellTypeMarkers" | |
| 248 #end if | |
| 249 #if str( $options.inferenceSvaNumMethod ) != "" | |
| 250 --inference-sva-num-method="$options.inferenceSvaNumMethod" | |
| 251 #end if | |
| 252 #if str( $options.exploratory ) == "True" | |
| 253 --exploratory | |
| 254 #end if | |
| 255 #if str( $options.exploratoryColumns ) != "" | |
| 256 --exploratory-columns="$options.exploratoryColumns" | |
| 257 #end if | |
| 258 #if str( $options.exploratoryTopDimensions ) != "" | |
| 259 --exploratory-top-dimensions="$options.exploratoryTopDimensions" | |
| 260 #end if | |
| 261 #if str( $options.exploratoryPrincipalComponents ) != "" | |
| 262 --exploratory-principal-components="$options.exploratoryPrincipalComponents" | |
| 263 #end if | |
| 264 #if str( $options.exploratoryCorrelationPvalueThreshold ) != "" | |
| 265 --exploratory-correlation-pvalue-threshold="$options.exploratoryCorrelationPvalueThreshold" | |
| 266 #end if | |
| 267 #if str( $options.exploratoryCorrelationPermutations ) != "" | |
| 268 --exploratory-correlation-permutations="$options.exploratoryCorrelationPermutations" | |
| 269 #end if | |
| 270 #if str( $options.exploratoryCorrelationQc ) == "True" | |
| 271 --exploratory-correlation-qc | |
| 272 #end if | |
| 273 #if str( $options.exploratoryBetaDistribution ) == "True" | |
| 274 --exploratory-beta-distribution | |
| 275 #end if | |
| 276 #if str( $options.exploratoryIntersample ) == "True" | |
| 277 --exploratory-intersample | |
| 278 #end if | |
| 279 #if str( $options.exploratoryDeviationPlots ) == "True" | |
| 280 --exploratory-deviation-plots | |
| 281 #end if | |
| 282 #if str( $options.exploratoryClustering ) != "" | |
| 283 --exploratory-clustering="$options.exploratoryClustering" | |
| 284 #end if | |
| 285 #if str( $options.exploratoryClusteringTopSites ) != "" | |
| 286 --exploratory-clustering-top-sites="$options.exploratoryClusteringTopSites" | |
| 287 #end if | |
| 288 #if str( $options.exploratoryRegionProfiles ) != "" | |
| 289 --exploratory-region-profiles="$options.exploratoryRegionProfiles" | |
| 290 #end if | |
| 291 #if str( $options.differential ) == "True" | |
| 292 --differential | |
| 293 #end if | |
| 294 #if str( $options.differentialSiteTestMethod ) != "" | |
| 295 --differential-site-test-method="$options.differentialSiteTestMethod" | |
| 296 #end if | |
| 297 #if str( $options.differentialPermutations ) != "" | |
| 298 --differential-permutations="$options.differentialPermutations" | |
| 299 #end if | |
| 300 #if str( $options.differentialComparisonColumns ) != "" | |
| 301 --differential-comparison-columns="$options.differentialComparisonColumns" | |
| 302 #end if | |
| 303 #if str( $options.differentialComparisonColumnsAllPairwise ) != "" | |
| 304 --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise" | |
| 305 #end if | |
| 306 #if str( $options.covariateAdjustmentColumns ) != "" | |
| 307 --covariate-adjustment-columns="$options.covariateAdjustmentColumns" | |
| 308 #end if | |
| 309 #if str( $options.differentialAdjustmentSva ) == "True" | |
| 310 --differential-adjustment-sva | |
| 311 #end if | |
| 312 #if str( $options.differentialAdjustmentCelltype ) == "True" | |
| 313 --differential-adjustment-celltype | |
| 314 #end if | |
| 315 #if str( $options.differentialEnrichment ) == "True" | |
| 316 --differential-enrichment | |
| 317 #end if | |
| 318 #if str( $options.exportToBed ) == "True" | |
| 319 --export-to-bed | |
| 320 #end if | |
| 321 #if str( $options.exportToTrackhub ) != "" | |
| 322 --export-to-trackhub="$options.exportToTrackhub" | |
| 323 #end if | |
| 324 #if str( $options.exportToCsv ) == "True" | |
| 325 --export-to-csv | |
| 326 #end if | |
| 327 #if str( $options.exportToEwasher ) == "True" | |
| 328 --export-to-ewasher | |
| 329 #end if | |
| 330 #if str( $options.exportTypes ) != "" | |
| 331 --export-types="$options.exportTypes" | |
| 332 #end if | |
| 333 #if str( $options.colorsMeth ) != "" | |
| 334 --colors-meth="$options.colorsMeth" | |
| 335 #end if | |
| 336 #if str( $options.colors3Gradient ) != "" | |
| 337 --colors-3-gradient="$options.colors3Gradient" | |
| 338 #end if | |
| 339 #if str( $options.loggingMemory ) == "True" | |
| 340 --logging-memory | |
| 341 #end if | |
| 342 #if str( $options.loggingDisk ) == "True" | |
| 343 --logging-disk | |
| 344 #end if | |
| 345 #if str( $options.loggingExitOnError ) == "True" | |
| 346 --logging-exit-on-error | |
| 347 #end if | |
| 348 #if str( $options.distributionSubsample ) != "" | |
| 349 --distribution-subsample="$options.distributionSubsample" | |
| 350 #end if | |
| 351 #if str( $options.diskDumpBigMatrices ) == "True" | |
| 352 --disk-dump-big-matrices | |
| 353 #end if | |
| 354 #if str( $options.enforceMemoryManagement ) == "True" | |
| 355 --enforce-memory-management | |
| 356 #end if | |
| 357 #if str( $options.enforceDestroyDiskDumps ) == "True" | |
| 358 --enforce-destroy-disk-dumps | |
| 359 #end if | |
| 360 #end if | |
| 361 </command> | |
| 362 <inputs> | |
| 363 <conditional name="inputDataSelector"> | |
| 364 <param name="dataType" type="select" label="Data Type"> | |
| 365 <option value="tables">Tabular data</option> | |
| 366 <option value="idats">IDAT files</option> | |
| 367 <option value="gsreport">GenomeStudio report</option> | |
| 368 <option value="geo">Gene Expression Omnibus series</option> | |
| 369 <option value="bed">BED files</option> | |
| 370 </param> | |
| 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 | |
| 667 <help> | |
| 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. | |
| 669 </help> | |
| 670 | |
| 671 <stdio> | |
| 672 <exit_code range="3:" level="fatal" description="Pipeline error" /> | |
| 673 </stdio> | |
| 674 | |
| 675 </tool> |