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author pavlo-lutsik
date Thu, 14 Aug 2014 14:56:18 -0400
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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>