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author pavlo-lutsik
date Sun, 21 Apr 2013 18:04:11 -0400
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12:73e7d00a9a19 13:d6cdc73fd57e
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( $inputDataSelector.dataType ) == "idats"
10 --pheno="$inputDataSelector.sampleAnnotations"
11 #end if
12 #if str( $inputDataSelector.dataType ) != "idats"
13 #pass
14 #else if str( $inputDataSelector.idatSelector.idatSource ) == "history"
15 --data-type="idatFiles"
16 #set $idatList=""
17 #for $input_file in $inputDataSelector.idatSelector.idatSeries:
18 #set $idatList+=str( $input_file.idatFile )
19 #set $idatList+=","
20 #end for
21 --idat-files="$idatList"
22 #else:
23 --data-type="idatDir"
24 --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path"
25 #end if
26 #if str( $inputDataSelector.dataType ) == "gsreport"
27 --data-type="GS.report"
28 --gs-report="$inputDataSelector.gsReportFile"
29 #end if
30 #if str( $inputDataSelector.dataType ) == "geo"
31 --data-type="GEO"
32 --geo-series=$inputDataSelector.geoSeries
33 #end if
34 #if str( $inputDataSelector.dataType ) == "tables"
35 --data-type="data.files"
36 --pheno="$inputDataSelector.sampleAnnotations"
37 #end if
38 #if str( $inputDataSelector.dataType ) == "tables"
39 --data-type="data.files"
40 --pheno="$inputDataSelector.sampleAnnotations"
41 --betas="$inputDataSelector.betaTable"
42 --pvals="$inputDataSelector.pvalTable"
43 #end if
44 #if str( $inputDataSelector.dataType ) == "bed"
45 --data-type="bed.dir"
46 --pheno="$inputDataSelector.sampleAnnotations"
47 #set $bedList=""
48 #for $input_file in $inputDataSelector.bedSeries:
49 #set $bedList+=str( $input_file.bedFile )
50 #set $bedList+=","
51 #end for
52 --bed-files="$bedList"
53 #end if
54 --report-dir="$html_file.extra_files_path"
55 --output-file="$html_file"
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>