Mercurial > repos > pavlo-lutsik > rnbeads
comparison rnbeads.xml @ 41:ebb026fa5f74 draft
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| author | pavlo-lutsik |
|---|---|
| date | Fri, 05 Jul 2013 17:23:02 -0400 |
| parents | aad84663f9c2 |
| children |
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| 40:bb2df76b44da | 41:ebb026fa5f74 |
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| 1 <?xml version="0.9"?> | |
| 2 <tool id="rnbeads" name="RnBeads" version="0.9"> | |
| 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="3.0.0">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( $options.identifiersColumn ) != "" | |
| 79 --identifiers-column="$options.identifiersColumn" | |
| 80 #end if | |
| 81 #if str( $options.pointsCategory ) != "" | |
| 82 --points-category="$options.pointsCategory" | |
| 83 #end if | |
| 84 #if str( $options.colorsCategory ) != "" | |
| 85 --colors-category="$options.colorsCategory" | |
| 86 #end if | |
| 87 #if str( $options.colorsGradient ) != "" | |
| 88 --colors-gradient="$options.colorsGradient" | |
| 89 #end if | |
| 90 #if str( $options.minGroupSize ) != "" | |
| 91 --min-group-size="$options.minGroupSize" | |
| 92 #end if | |
| 93 #if str( $options.maxGroupCount ) != "" | |
| 94 --max-group-count="$options.maxGroupCount" | |
| 95 #end if | |
| 96 #if str( $options.gzLargeFiles ) == "True" | |
| 97 --gz-large-files | |
| 98 #end if | |
| 99 #if str( $options.strandSpecific ) == "True" | |
| 100 --strand-specific | |
| 101 #end if | |
| 102 #if str( $options.replicateIdColumn ) != "" | |
| 103 --replicate-id-column="$options.replicateIdColumn" | |
| 104 #end if | |
| 105 #if str( $options.loadingNormalization ) == "True" | |
| 106 --loading-normalization | |
| 107 #end if | |
| 108 #if str( $options.loadingDefaultDataType ) != "" | |
| 109 --loading-default-data-type="$options.loadingDefaultDataType" | |
| 110 #end if | |
| 111 #if str( $options.loadingTableSeparator ) != "" | |
| 112 --loading-table-separator="$options.loadingTableSeparator" | |
| 113 #end if | |
| 114 #if str( $options.loadingBedStyle ) != "" | |
| 115 --loading-bed-style="$options.loadingBedStyle" | |
| 116 #end if | |
| 117 #if str( $options.loadingBedColumns ) != "" | |
| 118 --loading-bed-columns="$options.loadingBedColumns" | |
| 119 #end if | |
| 120 #if str( $options.loadingBedFrameShift ) != "" | |
| 121 --loading-bed-frame-shift="$options.loadingBedFrameShift" | |
| 122 #end if | |
| 123 #if str( $options.normalizationMethod ) != "" | |
| 124 --normalization-method="$options.normalizationMethod" | |
| 125 #end if | |
| 126 #if str( $options.normalizationBackgroundMethod ) != "" | |
| 127 --normalization-background-method="$options.normalizationBackgroundMethod" | |
| 128 #end if | |
| 129 #if str( $options.qc ) == "True" | |
| 130 --qc | |
| 131 #end if | |
| 132 #if str( $options.qcBoxplots ) == "True" | |
| 133 --qc-boxplots | |
| 134 #end if | |
| 135 #if str( $options.qcBarplots ) == "True" | |
| 136 --qc-barplots | |
| 137 #end if | |
| 138 #if str( $options.qcSnpHeatmap ) == "True" | |
| 139 --qc-snp-heatmap | |
| 140 #end if | |
| 141 #if str( $options.qcSnpHeatmap ) == "True" | |
| 142 --qc-snp-heatmap | |
| 143 #end if | |
| 144 #if str( $options.qcSnpBoxplot ) == "True" | |
| 145 --qc-snp-boxplot | |
| 146 #end if | |
| 147 #if str( $options.qcSnpBarplot ) == "True" | |
| 148 --qc-snp-barplot | |
| 149 #end if | |
| 150 #if str( $options.qcSampleBatchSize ) != "" | |
| 151 --qc-sample-batch-size="$options.qcSampleBatchSize" | |
| 152 #end if | |
| 153 #if str( $options.filteringContextRemoval ) != "" | |
| 154 --filtering-context-removal="$options.filteringContextRemoval" | |
| 155 #end if | |
| 156 #if str( $options.filteringSnp ) == "True" | |
| 157 --filtering-snp | |
| 158 #end if | |
| 159 #if str( $options.filteringSnpFrequency ) != "" | |
| 160 --filtering-snp-frequency="$options.filteringSnpFrequency" | |
| 161 #end if | |
| 162 #if str( $options.filteringSnpAccepted ) != "" | |
| 163 --filtering-snp-accepted="$options.filteringSnpAccepted" | |
| 164 #end if | |
| 165 #if str( $options.filteringSexChromosomesRemoval ) == "True" | |
| 166 --filtering-sex-chromosomes-removal | |
| 167 #end if | |
| 168 #if str( $options.filteringMissingValueQuantile ) != "" | |
| 169 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile" | |
| 170 #end if | |
| 171 #if str( $options.filteringCoverageThreshold ) != "" | |
| 172 --filtering-coverage-threshold="$options.filteringCoverageThreshold" | |
| 173 #end if | |
| 174 #if str( $options.filteringLowCoverageMasking ) == "True" | |
| 175 --filtering-low-coverage-masking | |
| 176 #end if | |
| 177 #if str( $options.filteringHighCoverageOutliers ) == "True" | |
| 178 --filtering-high-coverage-outliers | |
| 179 #end if | |
| 180 #if str( $options.filteringGreedycut ) == "True" | |
| 181 --filtering-greedycut | |
| 182 #end if | |
| 183 #if str( $options.filteringGreedycutPvalueThreshold ) != "" | |
| 184 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" | |
| 185 #end if | |
| 186 #if str( $options.filteringGreedycutRcTies ) != "" | |
| 187 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" | |
| 188 #end if | |
| 189 #if str( $options.filteringDeviationThreshold ) != "" | |
| 190 --filtering-deviation-threshold="$options.filteringDeviationThreshold" | |
| 191 #end if | |
| 192 #if str( $options.batch ) == "True" | |
| 193 --batch | |
| 194 #end if | |
| 195 #if str( $options.batchDreductionColumns ) != "" | |
| 196 --batch-dreduction-columns="$options.batchDreductionColumns" | |
| 197 #end if | |
| 198 #if str( $options.batchPrincipalComponents ) != "" | |
| 199 --batch-principal-components="$options.batchPrincipalComponents" | |
| 200 #end if | |
| 201 #if str( $options.batchCorrelationColumns ) != "" | |
| 202 --batch-correlation-columns="$options.batchCorrelationColumns" | |
| 203 #end if | |
| 204 #if str( $options.batchCorrelationPvalueThreshold ) != "" | |
| 205 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" | |
| 206 #end if | |
| 207 #if str( $options.batchCorrelationPermutations ) != "" | |
| 208 --batch-correlation-permutations="$options.batchCorrelationPermutations" | |
| 209 #end if | |
| 210 #if str( $options.batchCorrelationQc ) == "True" | |
| 211 --batch-correlation-qc | |
| 212 #end if | |
| 213 #if str( $options.profiles ) == "True" | |
| 214 --profiles | |
| 215 #end if | |
| 216 #if str( $options.profilesBetaDistribution ) == "True" | |
| 217 --profiles-beta-distribution | |
| 218 #end if | |
| 219 #if str( $options.profilesIntersample ) == "True" | |
| 220 --profiles-intersample | |
| 221 #end if | |
| 222 #if str( $options.profilesDeviationPlots ) == "True" | |
| 223 --profiles-deviation-plots | |
| 224 #end if | |
| 225 #if str( $options.profilesColumns ) != "" | |
| 226 --profiles-columns="$options.profilesColumns" | |
| 227 #end if | |
| 228 #if str( $options.profilesClustering ) == "True" | |
| 229 --profiles-clustering | |
| 230 #end if | |
| 231 #if str( $options.profilesClusteringTopProbes ) != "" | |
| 232 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes" | |
| 233 #end if | |
| 234 #if str( $options.regionProfilesTypes ) != "" | |
| 235 --region-profiles-types="$options.regionProfilesTypes" | |
| 236 #end if | |
| 237 #if str( $options.differential ) == "True" | |
| 238 --differential | |
| 239 #end if | |
| 240 #if str( $options.differentialPermutations ) != "" | |
| 241 --differential-permutations="$options.differentialPermutations" | |
| 242 #end if | |
| 243 #if str( $options.differentialComparisonColumns ) != "" | |
| 244 --differential-comparison-columns="$options.differentialComparisonColumns" | |
| 245 #end if | |
| 246 #if str( $options.differentialComparisonColumnsAllPairwise ) != "" | |
| 247 --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise" | |
| 248 #end if | |
| 249 #if str( $options.differentialEnrichment ) == "True" | |
| 250 --differential-enrichment | |
| 251 #end if | |
| 252 #if str( $options.exportToUcsc ) != "" | |
| 253 --export-to-ucsc="$options.exportToUcsc" | |
| 254 #end if | |
| 255 #if str( $options.exportToBed ) == "True" | |
| 256 --export-to-bed | |
| 257 #end if | |
| 258 #if str( $options.exportToCsv ) == "True" | |
| 259 --export-to-csv | |
| 260 #end if | |
| 261 #if str( $options.exportTypes ) != "" | |
| 262 --export-types="$options.exportTypes" | |
| 263 #end if | |
| 264 #if str( $options.colors3Gradient ) != "" | |
| 265 --colors-3-gradient="$options.colors3Gradient" | |
| 266 #end if | |
| 267 #if str( $options.loggingMemory ) == "True" | |
| 268 --logging-memory | |
| 269 #end if | |
| 270 #end if | |
| 271 </command> | |
| 272 <inputs> | |
| 273 <conditional name="inputDataSelector"> | |
| 274 <param name="dataType" type="select" label="Data Type"> | |
| 275 <option value="tables">Tabular data</option> | |
| 276 <option value="idats">IDAT files</option> | |
| 277 <option value="gsreport">GenomeStudio report</option> | |
| 278 <option value="geo">Gene Expression Omnibus series</option> | |
| 279 <option value="bed">BED files</option> | |
| 280 </param> | |
| 281 <when value="tables"> | |
| 282 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/> | |
| 283 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/> | |
| 284 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/> | |
| 285 </when> | |
| 286 <when value="idats"> | |
| 287 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/> | |
| 288 <conditional name="idatSelector"> | |
| 289 <param name="idatSource" type="select" label="IDAT source"> | |
| 290 <option value="history">Select from history</option> | |
| 291 <option value="repo">Repository on the server</option> | |
| 292 </param> | |
| 293 <when value="repo"> | |
| 294 <param name="idatRepo" type="select" label="Select an IDAT repository"> | |
| 295 <options from_data_table="rnbeads_repos"> | |
| 296 <filter type="sort_by" column="2" /> | |
| 297 <validator type="no_options" message="No repositories are available" /> | |
| 298 </options> | |
| 299 </param> | |
| 300 </when> | |
| 301 <when value="history"> | |
| 302 <repeat min="1" name="idatSeries" title="Input IDAT file"> | |
| 303 <param name="idatFile" type="data" format="idat" label="IDAT file"/> | |
| 304 </repeat> | |
| 305 </when> | |
| 306 </conditional> | |
| 307 </when> | |
| 308 <when value="gsreport"> | |
| 309 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" /> | |
| 310 </when> | |
| 311 <when value="geo"> | |
| 312 <param name="geoSeries" type="text" label="GEO series" /> | |
| 313 </when> | |
| 314 <when value="bed"> | |
| 315 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" /> | |
| 316 <repeat min="1" name="bedSeries" title="Input BED file"> | |
| 317 <param name="bedFile" type="data" format="bed" label="BED file"/> | |
| 318 </repeat> | |
| 319 </when> | |
| 320 </conditional> | |
| 321 <conditional name="options"> | |
| 322 <param name="optionSet" type="select" label="Options Set"> | |
| 323 <option value="default">Default options</option> | |
| 324 <option value="full">Full option set</option> | |
| 325 </param> | |
| 326 <when value="default" /> | |
| 327 <when value="full"> | |
| 328 <param name="analysisName" type="text" label="analysis.name, character" value=""/> | |
| 329 <param name="logging" type="select" label="logging, logical" value="1"> | |
| 330 <option value="True">True</option> | |
| 331 <option value="False">False</option> | |
| 332 </param> | |
| 333 <param name="email" type="text" label="email, character" value=""/> | |
| 334 <param name="assembly" type="text" label="assembly, character" value="hg19"/> | |
| 335 <param name="columnsPairing" type="text" label="columns.pairing, integer vector" value=""/> | |
| 336 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1"> | |
| 337 <option value="True">True</option> | |
| 338 <option value="False">False</option> | |
| 339 </param> | |
| 340 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/> | |
| 341 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/> | |
| 342 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/> | |
| 343 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/> | |
| 344 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/> | |
| 345 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/> | |
| 346 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/> | |
| 347 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0"> | |
| 348 <option value="True">True</option> | |
| 349 <option value="False">False</option> | |
| 350 </param> | |
| 351 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0"> | |
| 352 <option value="True">True</option> | |
| 353 <option value="False">False</option> | |
| 354 </param> | |
| 355 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/> | |
| 356 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1"> | |
| 357 <option value="True">True</option> | |
| 358 <option value="False">False</option> | |
| 359 </param> | |
| 360 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/> | |
| 361 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/> | |
| 362 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/> | |
| 363 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/> | |
| 364 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/> | |
| 365 <param name="normalizationMethod" type="text" label="normalization.method, character" value="swan"/> | |
| 366 <param name="normalizationBackgroundMethod" type="text" label="normalization.background.method, character" value="methylumi.noob"/> | |
| 367 <param name="qc" type="select" label="qc, logical" value="1"> | |
| 368 <option value="True">True</option> | |
| 369 <option value="False">False</option> | |
| 370 </param> | |
| 371 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1"> | |
| 372 <option value="True">True</option> | |
| 373 <option value="False">False</option> | |
| 374 </param> | |
| 375 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1"> | |
| 376 <option value="True">True</option> | |
| 377 <option value="False">False</option> | |
| 378 </param> | |
| 379 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1"> | |
| 380 <option value="True">True</option> | |
| 381 <option value="False">False</option> | |
| 382 </param> | |
| 383 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1"> | |
| 384 <option value="True">True</option> | |
| 385 <option value="False">False</option> | |
| 386 </param> | |
| 387 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0"> | |
| 388 <option value="True">True</option> | |
| 389 <option value="False">False</option> | |
| 390 </param> | |
| 391 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0"> | |
| 392 <option value="True">True</option> | |
| 393 <option value="False">False</option> | |
| 394 </param> | |
| 395 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="500"/> | |
| 396 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/> | |
| 397 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1"> | |
| 398 <option value="True">True</option> | |
| 399 <option value="False">False</option> | |
| 400 </param> | |
| 401 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/> | |
| 402 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/> | |
| 403 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0"> | |
| 404 <option value="True">True</option> | |
| 405 <option value="False">False</option> | |
| 406 </param> | |
| 407 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/> | |
| 408 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/> | |
| 409 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0"> | |
| 410 <option value="True">True</option> | |
| 411 <option value="False">False</option> | |
| 412 </param> | |
| 413 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0"> | |
| 414 <option value="True">True</option> | |
| 415 <option value="False">False</option> | |
| 416 </param> | |
| 417 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1"> | |
| 418 <option value="True">True</option> | |
| 419 <option value="False">False</option> | |
| 420 </param> | |
| 421 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/> | |
| 422 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/> | |
| 423 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/> | |
| 424 <param name="batch" type="select" label="batch, logical" value="1"> | |
| 425 <option value="True">True</option> | |
| 426 <option value="False">False</option> | |
| 427 </param> | |
| 428 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/> | |
| 429 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/> | |
| 430 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/> | |
| 431 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/> | |
| 432 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/> | |
| 433 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1"> | |
| 434 <option value="True">True</option> | |
| 435 <option value="False">False</option> | |
| 436 </param> | |
| 437 <param name="profiles" type="select" label="profiles, logical" value="1"> | |
| 438 <option value="True">True</option> | |
| 439 <option value="False">False</option> | |
| 440 </param> | |
| 441 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1"> | |
| 442 <option value="True">True</option> | |
| 443 <option value="False">False</option> | |
| 444 </param> | |
| 445 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1"> | |
| 446 <option value="True">True</option> | |
| 447 <option value="False">False</option> | |
| 448 </param> | |
| 449 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0"> | |
| 450 <option value="True">True</option> | |
| 451 <option value="False">False</option> | |
| 452 </param> | |
| 453 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/> | |
| 454 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1"> | |
| 455 <option value="True">True</option> | |
| 456 <option value="False">False</option> | |
| 457 </param> | |
| 458 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/> | |
| 459 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/> | |
| 460 <param name="differential" type="select" label="differential, logical" value="1"> | |
| 461 <option value="True">True</option> | |
| 462 <option value="False">False</option> | |
| 463 </param> | |
| 464 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/> | |
| 465 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/> | |
| 466 <param name="differentialComparisonColumnsAllPairwise" type="text" label="differential.comparison.columns.all.pairwise, integer vector" value=""/> | |
| 467 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0"> | |
| 468 <option value="True">True</option> | |
| 469 <option value="False">False</option> | |
| 470 </param> | |
| 471 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/> | |
| 472 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1"> | |
| 473 <option value="True">True</option> | |
| 474 <option value="False">False</option> | |
| 475 </param> | |
| 476 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0"> | |
| 477 <option value="True">True</option> | |
| 478 <option value="False">False</option> | |
| 479 </param> | |
| 480 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/> | |
| 481 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/> | |
| 482 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0"> | |
| 483 <option value="True">True</option> | |
| 484 <option value="False">False</option> | |
| 485 </param> | |
| 486 </when> | |
| 487 </conditional> | |
| 488 </inputs> | |
| 489 | |
| 490 <outputs> | |
| 491 <data format="html" name="html_file" label="index.html" /> | |
| 492 </outputs> | |
| 493 | |
| 494 <!-- | |
| 495 <tests> | |
| 496 <test> | |
| 497 <param name="input" value="fa_gc_content_input.fa"/> | |
| 498 <output name="out_file1" file="fa_gc_content_output.txt"/> | |
| 499 </test> | |
| 500 </tests> --> | |
| 501 | |
| 502 <help> | |
| 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. | |
| 504 </help> | |
| 505 | |
| 506 </tool> |