Mercurial > repos > pavlo-lutsik > rnbeads
comparison rnbeads.xml @ 0:d1d0d07a8af4 draft
First commit
| author | pavlo-lutsik |
|---|---|
| date | Wed, 17 Apr 2013 07:44:04 -0400 |
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| -1:000000000000 | 0:d1d0d07a8af4 |
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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="0.9">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 #if str( $inputDataSelector.dataType ) == "idat" | |
| 10 --data-type="idat.dir" | |
| 11 --pheno="$inputDataSelector.sampleAnnotations" | |
| 12 #if str( $idatSelector.idatSelector.idatSource ) == "history" | |
| 13 --idat-files ==" | |
| 14 #for $input_files in $inputDataSelector.input_series: | |
| 15 ${input_files.input_files}\t | |
| 16 #end for | |
| 17 " | |
| 18 #else: | |
| 19 --idat-files == "$idatRepo" | |
| 20 #end if | |
| 21 #end if | |
| 22 #if str( $inputDataSelector.dataType ) == "gsreport" | |
| 23 --data-type="GS.report" | |
| 24 --gs-report="$inputDataSelector.gsReportFile" | |
| 25 #end if | |
| 26 #if str( $inputDataSelector.dataType ) == "geo" | |
| 27 --data-type="GEO" | |
| 28 --geo-series=$inputDataSelector.geoSeries | |
| 29 #end if | |
| 30 #if str( $inputDataSelector.dataType ) == "tables" | |
| 31 --data-type="data.files" | |
| 32 --pheno="$inputDataSelector.sampleAnnotations" | |
| 33 #end if | |
| 34 #if str( $inputDataSelector.dataType ) == "tables" | |
| 35 --data-type="data.files" | |
| 36 --pheno="$inputDataSelector.sampleAnnotations" | |
| 37 --betas="$inputDataSelector.betaTable" | |
| 38 --pvals="$inputDataSelector.pvalTable" | |
| 39 #end if | |
| 40 #if str( $inputDataSelector.dataType ) == "bed" | |
| 41 --data-type="bed.dir" | |
| 42 --pheno="$inputDataSelector.sampleAnnotations" | |
| 43 --beds ==" | |
| 44 #for $input_files in $inputDataSelector.input_series: | |
| 45 ${input_files.input_files}\t | |
| 46 #end for | |
| 47 #end if | |
| 48 --report-dir="$html_file.files_path" | |
| 49 #if str( $options.optionSet ) == "full" | |
| 50 #if str( $options.analysisName ) != "" | |
| 51 --analysis-name = "$options.analysisName" | |
| 52 #end if | |
| 53 #if str( $options.logging ) == "True" | |
| 54 --logging | |
| 55 #end if | |
| 56 #if str( $options.email ) != "" | |
| 57 --email = "$options.email" | |
| 58 #end if | |
| 59 #if str( $options.assembly ) != "" | |
| 60 --assembly = "$options.assembly" | |
| 61 #end if | |
| 62 #if str( $options.analyzeSites ) == "True" | |
| 63 --analyze-sites | |
| 64 #end if | |
| 65 #if str( $options.regionTypes ) != "" | |
| 66 --region-types = "$options.regionTypes" | |
| 67 #end if | |
| 68 #if str( $options.identifiersColumn ) != "" | |
| 69 --identifiers-column = "$options.identifiersColumn" | |
| 70 #end if | |
| 71 #if str( $options.pointsCategory ) != "" | |
| 72 --points-category = "$options.pointsCategory" | |
| 73 #end if | |
| 74 #if str( $options.colorsCategory ) != "" | |
| 75 --colors-category = "$options.colorsCategory" | |
| 76 #end if | |
| 77 #if str( $options.colorsGradient ) != "" | |
| 78 --colors-gradient = "$options.colorsGradient" | |
| 79 #end if | |
| 80 #if str( $options.minGroupSize ) != "" | |
| 81 --min-group-size = "$options.minGroupSize" | |
| 82 #end if | |
| 83 #if str( $options.maxGroupCount ) != "" | |
| 84 --max-group-count = "$options.maxGroupCount" | |
| 85 #end if | |
| 86 #if str( $options.gzLargeFiles ) == "True" | |
| 87 --gz-large-files | |
| 88 #end if | |
| 89 #if str( $options.strandSpecific ) == "True" | |
| 90 --strand-specific | |
| 91 #end if | |
| 92 #if str( $options.replicateIdColumn ) != "" | |
| 93 --replicate-id-column = "$options.replicateIdColumn" | |
| 94 #end if | |
| 95 #if str( $options.loadingNormalization ) == "True" | |
| 96 --loading-normalization | |
| 97 #end if | |
| 98 #if str( $options.loadingDefaultDataType ) != "" | |
| 99 --loading-default-data-type = "$options.loadingDefaultDataType" | |
| 100 #end if | |
| 101 #if str( $options.loadingTableSeparator ) != "" | |
| 102 --loading-table-separator = "$options.loadingTableSeparator" | |
| 103 #end if | |
| 104 #if str( $options.loadingBedStyle ) != "" | |
| 105 --loading-bed-style = "$options.loadingBedStyle" | |
| 106 #end if | |
| 107 #if str( $options.loadingBedColumns ) != "" | |
| 108 --loading-bed-columns = "$options.loadingBedColumns" | |
| 109 #end if | |
| 110 #if str( $options.loadingBedFrameShift ) != "" | |
| 111 --loading-bed-frame-shift = "$options.loadingBedFrameShift" | |
| 112 #end if | |
| 113 #if str( $options.normalizationMethod ) != "" | |
| 114 --normalization-method = "$options.normalizationMethod" | |
| 115 #end if | |
| 116 #if str( $options.qc ) == "True" | |
| 117 --qc | |
| 118 #end if | |
| 119 #if str( $options.qcBoxplots ) == "True" | |
| 120 --qc-boxplots | |
| 121 #end if | |
| 122 #if str( $options.qcBarplots ) == "True" | |
| 123 --qc-barplots | |
| 124 #end if | |
| 125 #if str( $options.qcNegativeBoxplot ) == "True" | |
| 126 --qc-negative-boxplot | |
| 127 #end if | |
| 128 #if str( $options.qcSnpHeatmap ) == "True" | |
| 129 --qc-snp-heatmap | |
| 130 #end if | |
| 131 #if str( $options.qcSnpBoxplot ) == "True" | |
| 132 --qc-snp-boxplot | |
| 133 #end if | |
| 134 #if str( $options.qcSnpBarplot ) == "True" | |
| 135 --qc-snp-barplot | |
| 136 #end if | |
| 137 #if str( $options.qcSampleBatchSize ) != "" | |
| 138 --qc-sample-batch-size = "$options.qcSampleBatchSize" | |
| 139 #end if | |
| 140 #if str( $options.filteringContextRemoval ) != "" | |
| 141 --filtering-context-removal = "$options.filteringContextRemoval" | |
| 142 #end if | |
| 143 #if str( $options.filteringSnp ) == "True" | |
| 144 --filtering-snp | |
| 145 #end if | |
| 146 #if str( $options.filteringSnpFrequency ) != "" | |
| 147 --filtering-snp-frequency = "$options.filteringSnpFrequency" | |
| 148 #end if | |
| 149 #if str( $options.filteringSnpAccepted ) != "" | |
| 150 --filtering-snp-accepted = "$options.filteringSnpAccepted" | |
| 151 #end if | |
| 152 #if str( $options.filteringSexChromosomesRemoval ) == "True" | |
| 153 --filtering-sex-chromosomes-removal | |
| 154 #end if | |
| 155 #if str( $options.filteringMissingValueQuantile ) != "" | |
| 156 --filtering-missing-value-quantile = "$options.filteringMissingValueQuantile" | |
| 157 #end if | |
| 158 #if str( $options.filteringCoverageThreshold ) != "" | |
| 159 --filtering-coverage-threshold = "$options.filteringCoverageThreshold" | |
| 160 #end if | |
| 161 #if str( $options.filteringLowCoverageMasking ) == "True" | |
| 162 --filtering-low-coverage-masking | |
| 163 #end if | |
| 164 #if str( $options.filteringHighCoverageOutliers ) == "True" | |
| 165 --filtering-high-coverage-outliers | |
| 166 #end if | |
| 167 #if str( $options.filteringGreedycut ) == "True" | |
| 168 --filtering-greedycut | |
| 169 #end if | |
| 170 #if str( $options.filteringGreedycutPvalueThreshold ) != "" | |
| 171 --filtering-greedycut-pvalue-threshold = "$options.filteringGreedycutPvalueThreshold" | |
| 172 #end if | |
| 173 #if str( $options.filteringGreedycutRcTies ) != "" | |
| 174 --filtering-greedycut-rc-ties = "$options.filteringGreedycutRcTies" | |
| 175 #end if | |
| 176 #if str( $options.filteringDeviationThreshold ) != "" | |
| 177 --filtering-deviation-threshold = "$options.filteringDeviationThreshold" | |
| 178 #end if | |
| 179 #if str( $options.batch ) == "True" | |
| 180 --batch | |
| 181 #end if | |
| 182 #if str( $options.batchDreductionColumns ) != "" | |
| 183 --batch-dreduction-columns = "$options.batchDreductionColumns" | |
| 184 #end if | |
| 185 #if str( $options.batchPrincipalComponents ) != "" | |
| 186 --batch-principal-components = "$options.batchPrincipalComponents" | |
| 187 #end if | |
| 188 #if str( $options.batchCorrelationColumns ) != "" | |
| 189 --batch-correlation-columns = "$options.batchCorrelationColumns" | |
| 190 #end if | |
| 191 #if str( $options.batchCorrelationPvalueThreshold ) != "" | |
| 192 --batch-correlation-pvalue-threshold = "$options.batchCorrelationPvalueThreshold" | |
| 193 #end if | |
| 194 #if str( $options.batchCorrelationPermutations ) != "" | |
| 195 --batch-correlation-permutations = "$options.batchCorrelationPermutations" | |
| 196 #end if | |
| 197 #if str( $options.batchCorrelationQc ) == "True" | |
| 198 --batch-correlation-qc | |
| 199 #end if | |
| 200 #if str( $options.profiles ) == "True" | |
| 201 --profiles | |
| 202 #end if | |
| 203 #if str( $options.profilesBetaDistribution ) == "True" | |
| 204 --profiles-beta-distribution | |
| 205 #end if | |
| 206 #if str( $options.profilesIntersample ) == "True" | |
| 207 --profiles-intersample | |
| 208 #end if | |
| 209 #if str( $options.profilesDeviationPlots ) == "True" | |
| 210 --profiles-deviation-plots | |
| 211 #end if | |
| 212 #if str( $options.profilesColumns ) != "" | |
| 213 --profiles-columns = "$options.profilesColumns" | |
| 214 #end if | |
| 215 #if str( $options.profilesClustering ) == "True" | |
| 216 --profiles-clustering | |
| 217 #end if | |
| 218 #if str( $options.profilesClusteringTopProbes ) != "" | |
| 219 --profiles-clustering-top-probes = "$options.profilesClusteringTopProbes" | |
| 220 #end if | |
| 221 #if str( $options.regionProfilesTypes ) != "" | |
| 222 --region-profiles-types = "$options.regionProfilesTypes" | |
| 223 #end if | |
| 224 #if str( $options.differential ) == "True" | |
| 225 --differential | |
| 226 #end if | |
| 227 #if str( $options.differentialPermutations ) != "" | |
| 228 --differential-permutations = "$options.differentialPermutations" | |
| 229 #end if | |
| 230 #if str( $options.differentialComparisonColumns ) != "" | |
| 231 --differential-comparison-columns = "$options.differentialComparisonColumns" | |
| 232 #end if | |
| 233 #if str( $options.differentialEnrichment ) == "True" | |
| 234 --differential-enrichment | |
| 235 #end if | |
| 236 #if str( $options.exportToUcsc ) != "" | |
| 237 --export-to-ucsc = "$options.exportToUcsc" | |
| 238 #end if | |
| 239 #if str( $options.exportToBed ) == "True" | |
| 240 --export-to-bed | |
| 241 #end if | |
| 242 #if str( $options.exportToCsv ) == "True" | |
| 243 --export-to-csv | |
| 244 #end if | |
| 245 #if str( $options.exportTypes ) != "" | |
| 246 --export-types = "$options.exportTypes" | |
| 247 #end if | |
| 248 #if str( $options.colors3Gradient ) != "" | |
| 249 --colors-3-gradient = "$options.colors3Gradient" | |
| 250 #end if | |
| 251 #if str( $options.loggingMemory ) == "True" | |
| 252 --logging-memory | |
| 253 #end if | |
| 254 #if str( $options.usePstoimg ) == "True" | |
| 255 --use-pstoimg | |
| 256 #end if | |
| 257 #end if | |
| 258 </command> | |
| 259 <inputs> | |
| 260 <conditional name="inputDataSelector"> | |
| 261 <param name="dataType" type="select" label="Data Type"> | |
| 262 <option value="tables">Tabular data</option> | |
| 263 <option value="idats">IDAT files</option> | |
| 264 <option value="gsreport">GenomeStudio report</option> | |
| 265 <option value="geo">Gene Expression Omnibus series</option> | |
| 266 <option value="bed">BED files</option> | |
| 267 </param> | |
| 268 <when value="tables"> | |
| 269 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/> | |
| 270 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/> | |
| 271 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/> | |
| 272 </when> | |
| 273 <when value="idats"> | |
| 274 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/> | |
| 275 <conditional name="idatSelector"> | |
| 276 <param name="idatSource" type="select" label="IDAT source"> | |
| 277 <option value="history">Select from history</option> | |
| 278 <option value="repo">Repository on the server</option> | |
| 279 </param> | |
| 280 <when value="repo"> | |
| 281 <param name="idatRepo" type="select" label="Select an IDAT repository"> | |
| 282 <options from_data_table="rnbeads_repos"> | |
| 283 <filter type="sort_by" column="2" /> | |
| 284 <validator type="no_options" message="No repositories are available" /> | |
| 285 </options> | |
| 286 </param> | |
| 287 </when> | |
| 288 <when value="history"> | |
| 289 <repeat min="1" name="idatSeries" title="Input IDAT file"> | |
| 290 <param name="idatFiles" type="data" format="idat" label="IDAT file"/> | |
| 291 </repeat> | |
| 292 </when> | |
| 293 </conditional> | |
| 294 </when> | |
| 295 <when value="gsreport"> | |
| 296 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" /> | |
| 297 </when> | |
| 298 <when value="geo"> | |
| 299 <param name="geoSeries" type="text" label="GEO series" /> | |
| 300 </when> | |
| 301 <when value="bed"> | |
| 302 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" /> | |
| 303 <repeat min="1" name="bedSeries" title="Input BED file"> | |
| 304 <param name="idatFiles" type="data" format="idat"/> | |
| 305 </repeat> | |
| 306 </when> | |
| 307 </conditional> | |
| 308 <conditional name="options"> | |
| 309 <param name="optionSet" type="select" label="Options Set"> | |
| 310 <option value="default">Default options</option> | |
| 311 <option value="full">Full option set</option> | |
| 312 </param> | |
| 313 <when value="default" /> | |
| 314 <when value="full"> | |
| 315 <label>See package documentation for detailed description of each option</label> | |
| 316 <param name="analysisName" type="text" label="analysis.name, character" value=""/> | |
| 317 <param name="logging" type="select" label="logging, logical" value="1"> | |
| 318 <option value="True">True</option> | |
| 319 <option value="False">False</option> | |
| 320 </param> | |
| 321 <param name="email" type="text" label="email, character" value=""/> | |
| 322 <param name="assembly" type="text" label="assembly, character" value="hg19"/> | |
| 323 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1"> | |
| 324 <option value="True">True</option> | |
| 325 <option value="False">False</option> | |
| 326 </param> | |
| 327 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/> | |
| 328 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/> | |
| 329 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/> | |
| 330 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/> | |
| 331 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/> | |
| 332 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/> | |
| 333 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/> | |
| 334 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0"> | |
| 335 <option value="True">True</option> | |
| 336 <option value="False">False</option> | |
| 337 </param> | |
| 338 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0"> | |
| 339 <option value="True">True</option> | |
| 340 <option value="False">False</option> | |
| 341 </param> | |
| 342 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/> | |
| 343 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1"> | |
| 344 <option value="True">True</option> | |
| 345 <option value="False">False</option> | |
| 346 </param> | |
| 347 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/> | |
| 348 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/> | |
| 349 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/> | |
| 350 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/> | |
| 351 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/> | |
| 352 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/> | |
| 353 <param name="qc" type="select" label="qc, logical" value="1"> | |
| 354 <option value="True">True</option> | |
| 355 <option value="False">False</option> | |
| 356 </param> | |
| 357 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1"> | |
| 358 <option value="True">True</option> | |
| 359 <option value="False">False</option> | |
| 360 </param> | |
| 361 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1"> | |
| 362 <option value="True">True</option> | |
| 363 <option value="False">False</option> | |
| 364 </param> | |
| 365 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1"> | |
| 366 <option value="True">True</option> | |
| 367 <option value="False">False</option> | |
| 368 </param> | |
| 369 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1"> | |
| 370 <option value="True">True</option> | |
| 371 <option value="False">False</option> | |
| 372 </param> | |
| 373 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0"> | |
| 374 <option value="True">True</option> | |
| 375 <option value="False">False</option> | |
| 376 </param> | |
| 377 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0"> | |
| 378 <option value="True">True</option> | |
| 379 <option value="False">False</option> | |
| 380 </param> | |
| 381 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/> | |
| 382 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/> | |
| 383 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1"> | |
| 384 <option value="True">True</option> | |
| 385 <option value="False">False</option> | |
| 386 </param> | |
| 387 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/> | |
| 388 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/> | |
| 389 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0"> | |
| 390 <option value="True">True</option> | |
| 391 <option value="False">False</option> | |
| 392 </param> | |
| 393 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/> | |
| 394 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/> | |
| 395 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0"> | |
| 396 <option value="True">True</option> | |
| 397 <option value="False">False</option> | |
| 398 </param> | |
| 399 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0"> | |
| 400 <option value="True">True</option> | |
| 401 <option value="False">False</option> | |
| 402 </param> | |
| 403 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1"> | |
| 404 <option value="True">True</option> | |
| 405 <option value="False">False</option> | |
| 406 </param> | |
| 407 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/> | |
| 408 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/> | |
| 409 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/> | |
| 410 <param name="batch" type="select" label="batch, logical" value="1"> | |
| 411 <option value="True">True</option> | |
| 412 <option value="False">False</option> | |
| 413 </param> | |
| 414 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/> | |
| 415 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/> | |
| 416 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/> | |
| 417 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/> | |
| 418 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/> | |
| 419 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1"> | |
| 420 <option value="True">True</option> | |
| 421 <option value="False">False</option> | |
| 422 </param> | |
| 423 <param name="profiles" type="select" label="profiles, logical" value="1"> | |
| 424 <option value="True">True</option> | |
| 425 <option value="False">False</option> | |
| 426 </param> | |
| 427 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1"> | |
| 428 <option value="True">True</option> | |
| 429 <option value="False">False</option> | |
| 430 </param> | |
| 431 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1"> | |
| 432 <option value="True">True</option> | |
| 433 <option value="False">False</option> | |
| 434 </param> | |
| 435 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0"> | |
| 436 <option value="True">True</option> | |
| 437 <option value="False">False</option> | |
| 438 </param> | |
| 439 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/> | |
| 440 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1"> | |
| 441 <option value="True">True</option> | |
| 442 <option value="False">False</option> | |
| 443 </param> | |
| 444 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/> | |
| 445 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/> | |
| 446 <param name="differential" type="select" label="differential, logical" value="1"> | |
| 447 <option value="True">True</option> | |
| 448 <option value="False">False</option> | |
| 449 </param> | |
| 450 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/> | |
| 451 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/> | |
| 452 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0"> | |
| 453 <option value="True">True</option> | |
| 454 <option value="False">False</option> | |
| 455 </param> | |
| 456 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/> | |
| 457 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1"> | |
| 458 <option value="True">True</option> | |
| 459 <option value="False">False</option> | |
| 460 </param> | |
| 461 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0"> | |
| 462 <option value="True">True</option> | |
| 463 <option value="False">False</option> | |
| 464 </param> | |
| 465 <param name="exportTypes" type="text" label="export.types, character vector" value=""/> | |
| 466 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/> | |
| 467 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0"> | |
| 468 <option value="True">True</option> | |
| 469 <option value="False">False</option> | |
| 470 </param> | |
| 471 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0"> | |
| 472 <option value="True">True</option> | |
| 473 <option value="False">False</option> | |
| 474 </param> | |
| 475 </when> | |
| 476 </conditional> | |
| 477 </inputs> | |
| 478 | |
| 479 <outputs> | |
| 480 <data format="html" name="html_file" label="index.html" /> | |
| 481 </outputs> | |
| 482 | |
| 483 <!-- | |
| 484 <tests> | |
| 485 <test> | |
| 486 <param name="input" value="fa_gc_content_input.fa"/> | |
| 487 <output name="out_file1" file="fa_gc_content_output.txt"/> | |
| 488 </test> | |
| 489 </tests> --> | |
| 490 | |
| 491 <help> | |
| 492 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. | |
| 493 </help> | |
| 494 | |
| 495 </tool> |