|
15
|
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 --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.analyzeSites ) == "True"
|
|
|
70 --analyze-sites
|
|
|
71 #end if
|
|
|
72 #if str( $options.regionTypes ) != ""
|
|
|
73 --region-types="$options.regionTypes"
|
|
|
74 #end if
|
|
|
75 #if str( $options.identifiersColumn ) != ""
|
|
|
76 --identifiers-column="$options.identifiersColumn"
|
|
|
77 #end if
|
|
|
78 #if str( $options.pointsCategory ) != ""
|
|
|
79 --points-category="$options.pointsCategory"
|
|
|
80 #end if
|
|
|
81 #if str( $options.colorsCategory ) != ""
|
|
|
82 --colors-category="$options.colorsCategory"
|
|
|
83 #end if
|
|
|
84 #if str( $options.colorsGradient ) != ""
|
|
|
85 --colors-gradient="$options.colorsGradient"
|
|
|
86 #end if
|
|
|
87 #if str( $options.minGroupSize ) != ""
|
|
|
88 --min-group-size="$options.minGroupSize"
|
|
|
89 #end if
|
|
|
90 #if str( $options.maxGroupCount ) != ""
|
|
|
91 --max-group-count="$options.maxGroupCount"
|
|
|
92 #end if
|
|
|
93 #if str( $options.gzLargeFiles ) == "True"
|
|
|
94 --gz-large-files
|
|
|
95 #end if
|
|
|
96 #if str( $options.strandSpecific ) == "True"
|
|
|
97 --strand-specific
|
|
|
98 #end if
|
|
|
99 #if str( $options.replicateIdColumn ) != ""
|
|
|
100 --replicate-id-column="$options.replicateIdColumn"
|
|
|
101 #end if
|
|
|
102 #if str( $options.loadingNormalization ) == "True"
|
|
|
103 --loading-normalization
|
|
|
104 #end if
|
|
|
105 #if str( $options.loadingDefaultDataType ) != ""
|
|
|
106 --loading-default-data-type="$options.loadingDefaultDataType"
|
|
|
107 #end if
|
|
|
108 #if str( $options.loadingTableSeparator ) != ""
|
|
|
109 --loading-table-separator="$options.loadingTableSeparator"
|
|
|
110 #end if
|
|
|
111 #if str( $options.loadingBedStyle ) != ""
|
|
|
112 --loading-bed-style="$options.loadingBedStyle"
|
|
|
113 #end if
|
|
|
114 #if str( $options.loadingBedColumns ) != ""
|
|
|
115 --loading-bed-columns="$options.loadingBedColumns"
|
|
|
116 #end if
|
|
|
117 #if str( $options.loadingBedFrameShift ) != ""
|
|
|
118 --loading-bed-frame-shift="$options.loadingBedFrameShift"
|
|
|
119 #end if
|
|
|
120 #if str( $options.normalizationMethod ) != ""
|
|
|
121 --normalization-method="$options.normalizationMethod"
|
|
|
122 #end if
|
|
|
123 #if str( $options.normalizationSubtractBackground ) == "True"
|
|
|
124 --normalization-subtract-background
|
|
|
125 #end if
|
|
|
126 #if str( $options.qc ) == "True"
|
|
|
127 --qc
|
|
|
128 #end if
|
|
|
129 #if str( $options.qcBoxplots ) == "True"
|
|
|
130 --qc-boxplots
|
|
|
131 #end if
|
|
|
132 #if str( $options.qcBarplots ) == "True"
|
|
|
133 --qc-barplots
|
|
|
134 #end if
|
|
|
135 #if str( $options.qcNegativeBoxplot ) == "True"
|
|
|
136 --qc-negative-boxplot
|
|
|
137 #end if
|
|
|
138 #if str( $options.qcSnpHeatmap ) == "True"
|
|
|
139 --qc-snp-heatmap
|
|
|
140 #end if
|
|
|
141 #if str( $options.qcSnpBoxplot ) == "True"
|
|
|
142 --qc-snp-boxplot
|
|
|
143 #end if
|
|
|
144 #if str( $options.qcSnpBarplot ) == "True"
|
|
|
145 --qc-snp-barplot
|
|
|
146 #end if
|
|
|
147 #if str( $options.qcSampleBatchSize ) != ""
|
|
|
148 --qc-sample-batch-size="$options.qcSampleBatchSize"
|
|
|
149 #end if
|
|
|
150 #if str( $options.filteringContextRemoval ) != ""
|
|
|
151 --filtering-context-removal="$options.filteringContextRemoval"
|
|
|
152 #end if
|
|
|
153 #if str( $options.filteringSnp ) == "True"
|
|
|
154 --filtering-snp
|
|
|
155 #end if
|
|
|
156 #if str( $options.filteringSnpFrequency ) != ""
|
|
|
157 --filtering-snp-frequency="$options.filteringSnpFrequency"
|
|
|
158 #end if
|
|
|
159 #if str( $options.filteringSnpAccepted ) != ""
|
|
|
160 --filtering-snp-accepted="$options.filteringSnpAccepted"
|
|
|
161 #end if
|
|
|
162 #if str( $options.filteringSexChromosomesRemoval ) == "True"
|
|
|
163 --filtering-sex-chromosomes-removal
|
|
|
164 #end if
|
|
|
165 #if str( $options.filteringMissingValueQuantile ) != ""
|
|
|
166 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
|
|
|
167 #end if
|
|
|
168 #if str( $options.filteringCoverageThreshold ) != ""
|
|
|
169 --filtering-coverage-threshold="$options.filteringCoverageThreshold"
|
|
|
170 #end if
|
|
|
171 #if str( $options.filteringLowCoverageMasking ) == "True"
|
|
|
172 --filtering-low-coverage-masking
|
|
|
173 #end if
|
|
|
174 #if str( $options.filteringHighCoverageOutliers ) == "True"
|
|
|
175 --filtering-high-coverage-outliers
|
|
|
176 #end if
|
|
|
177 #if str( $options.filteringGreedycut ) == "True"
|
|
|
178 --filtering-greedycut
|
|
|
179 #end if
|
|
|
180 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
|
|
|
181 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
|
|
|
182 #end if
|
|
|
183 #if str( $options.filteringGreedycutRcTies ) != ""
|
|
|
184 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
|
|
|
185 #end if
|
|
|
186 #if str( $options.filteringDeviationThreshold ) != ""
|
|
|
187 --filtering-deviation-threshold="$options.filteringDeviationThreshold"
|
|
|
188 #end if
|
|
|
189 #if str( $options.batch ) == "True"
|
|
|
190 --batch
|
|
|
191 #end if
|
|
|
192 #if str( $options.batchDreductionColumns ) != ""
|
|
|
193 --batch-dreduction-columns="$options.batchDreductionColumns"
|
|
|
194 #end if
|
|
|
195 #if str( $options.batchPrincipalComponents ) != ""
|
|
|
196 --batch-principal-components="$options.batchPrincipalComponents"
|
|
|
197 #end if
|
|
|
198 #if str( $options.batchCorrelationColumns ) != ""
|
|
|
199 --batch-correlation-columns="$options.batchCorrelationColumns"
|
|
|
200 #end if
|
|
|
201 #if str( $options.batchCorrelationPvalueThreshold ) != ""
|
|
|
202 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold"
|
|
|
203 #end if
|
|
|
204 #if str( $options.batchCorrelationPermutations ) != ""
|
|
|
205 --batch-correlation-permutations="$options.batchCorrelationPermutations"
|
|
|
206 #end if
|
|
|
207 #if str( $options.batchCorrelationQc ) == "True"
|
|
|
208 --batch-correlation-qc
|
|
|
209 #end if
|
|
|
210 #if str( $options.profiles ) == "True"
|
|
|
211 --profiles
|
|
|
212 #end if
|
|
|
213 #if str( $options.profilesBetaDistribution ) == "True"
|
|
|
214 --profiles-beta-distribution
|
|
|
215 #end if
|
|
|
216 #if str( $options.profilesIntersample ) == "True"
|
|
|
217 --profiles-intersample
|
|
|
218 #end if
|
|
|
219 #if str( $options.profilesDeviationPlots ) == "True"
|
|
|
220 --profiles-deviation-plots
|
|
|
221 #end if
|
|
|
222 #if str( $options.profilesColumns ) != ""
|
|
|
223 --profiles-columns="$options.profilesColumns"
|
|
|
224 #end if
|
|
|
225 #if str( $options.profilesClustering ) == "True"
|
|
|
226 --profiles-clustering
|
|
|
227 #end if
|
|
|
228 #if str( $options.profilesClusteringTopProbes ) != ""
|
|
|
229 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes"
|
|
|
230 #end if
|
|
|
231 #if str( $options.regionProfilesTypes ) != ""
|
|
|
232 --region-profiles-types="$options.regionProfilesTypes"
|
|
|
233 #end if
|
|
|
234 #if str( $options.differential ) == "True"
|
|
|
235 --differential
|
|
|
236 #end if
|
|
|
237 #if str( $options.differentialPermutations ) != ""
|
|
|
238 --differential-permutations="$options.differentialPermutations"
|
|
|
239 #end if
|
|
|
240 #if str( $options.differentialComparisonColumns ) != ""
|
|
|
241 --differential-comparison-columns="$options.differentialComparisonColumns"
|
|
|
242 #end if
|
|
|
243 #if str( $options.differentialEnrichment ) == "True"
|
|
|
244 --differential-enrichment
|
|
|
245 #end if
|
|
|
246 #if str( $options.exportToUcsc ) != ""
|
|
|
247 --export-to-ucsc="$options.exportToUcsc"
|
|
|
248 #end if
|
|
|
249 #if str( $options.exportToBed ) == "True"
|
|
|
250 --export-to-bed
|
|
|
251 #end if
|
|
|
252 #if str( $options.exportToCsv ) == "True"
|
|
|
253 --export-to-csv
|
|
|
254 #end if
|
|
|
255 #if str( $options.exportTypes ) != ""
|
|
|
256 --export-types="$options.exportTypes"
|
|
|
257 #end if
|
|
|
258 #if str( $options.colors3Gradient ) != ""
|
|
|
259 --colors-3-gradient="$options.colors3Gradient"
|
|
|
260 #end if
|
|
|
261 #if str( $options.loggingMemory ) == "True"
|
|
|
262 --logging-memory
|
|
|
263 #end if
|
|
|
264 #if str( $options.usePstoimg ) == "True"
|
|
|
265 --use-pstoimg
|
|
|
266 #end if
|
|
|
267 #end if
|
|
|
268 </command>
|
|
|
269 <inputs>
|
|
|
270 <conditional name="inputDataSelector">
|
|
|
271 <param name="dataType" type="select" label="Data Type">
|
|
|
272 <option value="tables">Tabular data</option>
|
|
|
273 <option value="idats">IDAT files</option>
|
|
|
274 <option value="gsreport">GenomeStudio report</option>
|
|
|
275 <option value="geo">Gene Expression Omnibus series</option>
|
|
|
276 <option value="bed">BED files</option>
|
|
|
277 </param>
|
|
|
278 <when value="tables">
|
|
|
279 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
|
|
|
280 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
|
|
|
281 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
|
|
|
282 </when>
|
|
|
283 <when value="idats">
|
|
|
284 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
|
|
|
285 <conditional name="idatSelector">
|
|
|
286 <param name="idatSource" type="select" label="IDAT source">
|
|
|
287 <option value="history">Select from history</option>
|
|
|
288 <option value="repo">Repository on the server</option>
|
|
|
289 </param>
|
|
|
290 <when value="repo">
|
|
|
291 <param name="idatRepo" type="select" label="Select an IDAT repository">
|
|
|
292 <options from_data_table="rnbeads_repos">
|
|
|
293 <filter type="sort_by" column="2" />
|
|
|
294 <validator type="no_options" message="No repositories are available" />
|
|
|
295 </options>
|
|
|
296 </param>
|
|
|
297 </when>
|
|
|
298 <when value="history">
|
|
|
299 <repeat min="1" name="idatSeries" title="Input IDAT file">
|
|
|
300 <param name="idatFile" type="data" format="idat" label="IDAT file"/>
|
|
|
301 </repeat>
|
|
|
302 </when>
|
|
|
303 </conditional>
|
|
|
304 </when>
|
|
|
305 <when value="gsreport">
|
|
|
306 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
|
|
|
307 </when>
|
|
|
308 <when value="geo">
|
|
|
309 <param name="geoSeries" type="text" label="GEO series" />
|
|
|
310 </when>
|
|
|
311 <when value="bed">
|
|
|
312 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
|
|
|
313 <repeat min="1" name="bedSeries" title="Input BED file">
|
|
|
314 <param name="bedFile" type="data" format="bed" label="BED file"/>
|
|
|
315 </repeat>
|
|
|
316 </when>
|
|
|
317 </conditional>
|
|
|
318 <conditional name="options">
|
|
|
319 <param name="optionSet" type="select" label="Options Set">
|
|
|
320 <option value="default">Default options</option>
|
|
|
321 <option value="full">Full option set</option>
|
|
|
322 </param>
|
|
|
323 <when value="default" />
|
|
|
324 <when value="full">
|
|
|
325 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
|
|
|
326 <param name="logging" type="select" label="logging, logical" value="1">
|
|
|
327 <option value="True">True</option>
|
|
|
328 <option value="False">False</option>
|
|
|
329 </param>
|
|
|
330 <param name="email" type="text" label="email, character" value=""/>
|
|
|
331 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
|
|
|
332 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
|
|
|
333 <option value="True">True</option>
|
|
|
334 <option value="False">False</option>
|
|
|
335 </param>
|
|
|
336 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
|
|
|
337 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
|
|
|
338 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
|
|
|
339 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
|
|
|
340 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
|
|
|
341 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
|
|
|
342 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
|
|
|
343 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
|
|
|
344 <option value="True">True</option>
|
|
|
345 <option value="False">False</option>
|
|
|
346 </param>
|
|
|
347 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
|
|
|
348 <option value="True">True</option>
|
|
|
349 <option value="False">False</option>
|
|
|
350 </param>
|
|
|
351 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
|
|
|
352 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
|
|
|
353 <option value="True">True</option>
|
|
|
354 <option value="False">False</option>
|
|
|
355 </param>
|
|
|
356 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
|
|
|
357 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/>
|
|
|
358 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
|
|
|
359 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
|
|
|
360 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
|
|
|
361 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/>
|
|
|
362 <param name="normalizationSubtractBackground" type="select" label="normalization.subtract.background, logical" value="0">
|
|
|
363 <option value="True">True</option>
|
|
|
364 <option value="False">False</option>
|
|
|
365 </param>
|
|
|
366 <param name="qc" type="select" label="qc, logical" value="1">
|
|
|
367 <option value="True">True</option>
|
|
|
368 <option value="False">False</option>
|
|
|
369 </param>
|
|
|
370 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
|
|
|
371 <option value="True">True</option>
|
|
|
372 <option value="False">False</option>
|
|
|
373 </param>
|
|
|
374 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
|
|
|
375 <option value="True">True</option>
|
|
|
376 <option value="False">False</option>
|
|
|
377 </param>
|
|
|
378 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
|
|
|
379 <option value="True">True</option>
|
|
|
380 <option value="False">False</option>
|
|
|
381 </param>
|
|
|
382 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
|
|
|
383 <option value="True">True</option>
|
|
|
384 <option value="False">False</option>
|
|
|
385 </param>
|
|
|
386 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
|
|
|
387 <option value="True">True</option>
|
|
|
388 <option value="False">False</option>
|
|
|
389 </param>
|
|
|
390 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
|
|
|
391 <option value="True">True</option>
|
|
|
392 <option value="False">False</option>
|
|
|
393 </param>
|
|
|
394 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/>
|
|
|
395 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
|
|
|
396 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
|
|
|
397 <option value="True">True</option>
|
|
|
398 <option value="False">False</option>
|
|
|
399 </param>
|
|
|
400 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
|
|
|
401 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
|
|
|
402 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
|
|
|
403 <option value="True">True</option>
|
|
|
404 <option value="False">False</option>
|
|
|
405 </param>
|
|
|
406 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
|
|
|
407 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
|
|
|
408 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
|
|
|
409 <option value="True">True</option>
|
|
|
410 <option value="False">False</option>
|
|
|
411 </param>
|
|
|
412 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
|
|
|
413 <option value="True">True</option>
|
|
|
414 <option value="False">False</option>
|
|
|
415 </param>
|
|
|
416 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
|
|
|
417 <option value="True">True</option>
|
|
|
418 <option value="False">False</option>
|
|
|
419 </param>
|
|
|
420 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
|
|
|
421 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
|
|
|
422 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
|
|
|
423 <param name="batch" type="select" label="batch, logical" value="1">
|
|
|
424 <option value="True">True</option>
|
|
|
425 <option value="False">False</option>
|
|
|
426 </param>
|
|
|
427 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
|
|
|
428 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
|
|
|
429 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
|
|
|
430 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
|
|
|
431 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
|
|
|
432 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
|
|
|
433 <option value="True">True</option>
|
|
|
434 <option value="False">False</option>
|
|
|
435 </param>
|
|
|
436 <param name="profiles" type="select" label="profiles, logical" value="1">
|
|
|
437 <option value="True">True</option>
|
|
|
438 <option value="False">False</option>
|
|
|
439 </param>
|
|
|
440 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
|
|
|
441 <option value="True">True</option>
|
|
|
442 <option value="False">False</option>
|
|
|
443 </param>
|
|
|
444 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
|
|
|
445 <option value="True">True</option>
|
|
|
446 <option value="False">False</option>
|
|
|
447 </param>
|
|
|
448 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
|
|
|
449 <option value="True">True</option>
|
|
|
450 <option value="False">False</option>
|
|
|
451 </param>
|
|
|
452 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
|
|
|
453 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
|
|
|
454 <option value="True">True</option>
|
|
|
455 <option value="False">False</option>
|
|
|
456 </param>
|
|
|
457 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
|
|
|
458 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
|
|
|
459 <param name="differential" type="select" label="differential, logical" value="1">
|
|
|
460 <option value="True">True</option>
|
|
|
461 <option value="False">False</option>
|
|
|
462 </param>
|
|
|
463 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
|
|
|
464 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
|
|
|
465 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
|
|
|
466 <option value="True">True</option>
|
|
|
467 <option value="False">False</option>
|
|
|
468 </param>
|
|
|
469 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
|
|
|
470 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
|
|
|
471 <option value="True">True</option>
|
|
|
472 <option value="False">False</option>
|
|
|
473 </param>
|
|
|
474 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
|
|
|
475 <option value="True">True</option>
|
|
|
476 <option value="False">False</option>
|
|
|
477 </param>
|
|
|
478 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
|
|
|
479 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
|
|
|
480 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
|
|
|
481 <option value="True">True</option>
|
|
|
482 <option value="False">False</option>
|
|
|
483 </param>
|
|
|
484 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
|
|
|
485 <option value="True">True</option>
|
|
|
486 <option value="False">False</option>
|
|
|
487 </param>
|
|
|
488 </when>
|
|
|
489 </conditional>
|
|
|
490 </inputs>
|
|
|
491
|
|
|
492 <outputs>
|
|
|
493 <data format="html" name="html_file" label="index.html" />
|
|
|
494 </outputs>
|
|
|
495
|
|
|
496 <!--
|
|
|
497 <tests>
|
|
|
498 <test>
|
|
|
499 <param name="input" value="fa_gc_content_input.fa"/>
|
|
|
500 <output name="out_file1" file="fa_gc_content_output.txt"/>
|
|
|
501 </test>
|
|
|
502 </tests> -->
|
|
|
503
|
|
|
504 <help>
|
|
|
505 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.
|
|
|
506 </help>
|
|
|
507
|
|
|
508 </tool> |
