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comparison rnbeads.xml @ 43:39b78c48d064 draft

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author pavlo-lutsik
date Fri, 05 Jul 2013 17:39:25 -0400
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42:16f6ef2b3251 43:39b78c48d064
1 <?xml version="0.9"?>
2 <tool id="rnbeads" name="RnBeads" version="0.9">
3 <description>Performs RnBeads analysis for the selected set of </description>
4 <requirements>
5 <requirement type="set_environment" version="1.0">R_SCRIPTS_PATH</requirement>
6 <requirement type="package" version="3.0.0">R</requirement>
7 </requirements>
8 <command interpreter="bash">rnbeads_galaxy_wrapper.sh
9 --report-dir="$html_file.extra_files_path"
10 --output-file="$html_file"
11 #if str( $inputDataSelector.dataType ) == "idats"
12 --pheno="$inputDataSelector.sampleAnnotations"
13 #end if
14 #if str( $inputDataSelector.dataType ) != "idats"
15 #pass
16 #else if str( $inputDataSelector.idatSelector.idatSource ) == "history"
17 --data-type="idatFiles"
18 #set $idatList=""
19 #for $input_file in $inputDataSelector.idatSelector.idatSeries:
20 #set $idatList+=str( $input_file.idatFile )
21 #set $idatList+=","
22 #end for
23 --idat-files="$idatList"
24 #else:
25 --data-type="idatDir"
26 --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path"
27 #end if
28 #if str( $inputDataSelector.dataType ) == "gsreport"
29 --data-type="GS.report"
30 --gs-report="$inputDataSelector.gsReportFile"
31 #end if
32 #if str( $inputDataSelector.dataType ) == "geo"
33 --data-type="GEO"
34 --geo-series=$inputDataSelector.geoSeries
35 #end if
36 #if str( $inputDataSelector.dataType ) == "tables"
37 --data-type="data.files"
38 --pheno="$inputDataSelector.sampleAnnotations"
39 #end if
40 #if str( $inputDataSelector.dataType ) == "tables"
41 --data-type="data.files"
42 --pheno="$inputDataSelector.sampleAnnotations"
43 --betas="$inputDataSelector.betaTable"
44 --pvals="$inputDataSelector.pvalTable"
45 #end if
46 #if str( $inputDataSelector.dataType ) == "bed"
47 --data-type="bed.dir"
48 --pheno="$inputDataSelector.sampleAnnotations"
49 #set $bedList=""
50 #for $input_file in $inputDataSelector.bedSeries:
51 #set $bedList+=str( $input_file.bedFile )
52 #set $bedList+=","
53 #end for
54 --bed-files="$bedList"
55 #end if
56 #if str( $options.optionSet ) == "full"
57 #if str( $options.analysisName ) != ""
58 --analysis-name="$options.analysisName"
59 #end if
60 #if str( $options.logging ) == "True"
61 --logging
62 #end if
63 #if str( $options.email ) != ""
64 --email="$options.email"
65 #end if
66 #if str( $options.assembly ) != ""
67 --assembly="$options.assembly"
68 #end if
69 #if str( $options.columnsPairing ) != ""
70 --columns-pairing="$options.columnsPairing"
71 #end if
72 #if str( $options.analyzeSites ) == "True"
73 --analyze-sites
74 #end if
75 #if str( $options.regionTypes ) != ""
76 --region-types="$options.regionTypes"
77 #end if
78 #if str( $options.identifiersColumn ) != ""
79 --identifiers-column="$options.identifiersColumn"
80 #end if
81 #if str( $options.pointsCategory ) != ""
82 --points-category="$options.pointsCategory"
83 #end if
84 #if str( $options.colorsCategory ) != ""
85 --colors-category="$options.colorsCategory"
86 #end if
87 #if str( $options.colorsGradient ) != ""
88 --colors-gradient="$options.colorsGradient"
89 #end if
90 #if str( $options.minGroupSize ) != ""
91 --min-group-size="$options.minGroupSize"
92 #end if
93 #if str( $options.maxGroupCount ) != ""
94 --max-group-count="$options.maxGroupCount"
95 #end if
96 #if str( $options.gzLargeFiles ) == "True"
97 --gz-large-files
98 #end if
99 #if str( $options.strandSpecific ) == "True"
100 --strand-specific
101 #end if
102 #if str( $options.replicateIdColumn ) != ""
103 --replicate-id-column="$options.replicateIdColumn"
104 #end if
105 #if str( $options.loadingNormalization ) == "True"
106 --loading-normalization
107 #end if
108 #if str( $options.loadingDefaultDataType ) != ""
109 --loading-default-data-type="$options.loadingDefaultDataType"
110 #end if
111 #if str( $options.loadingTableSeparator ) != ""
112 --loading-table-separator="$options.loadingTableSeparator"
113 #end if
114 #if str( $options.loadingBedStyle ) != ""
115 --loading-bed-style="$options.loadingBedStyle"
116 #end if
117 #if str( $options.loadingBedColumns ) != ""
118 --loading-bed-columns="$options.loadingBedColumns"
119 #end if
120 #if str( $options.loadingBedFrameShift ) != ""
121 --loading-bed-frame-shift="$options.loadingBedFrameShift"
122 #end if
123 #if str( $options.normalizationMethod ) != ""
124 --normalization-method="$options.normalizationMethod"
125 #end if
126 #if str( $options.normalizationBackgroundMethod ) != ""
127 --normalization-background-method="$options.normalizationBackgroundMethod"
128 #end if
129 #if str( $options.qc ) == "True"
130 --qc
131 #end if
132 #if str( $options.qcBoxplots ) == "True"
133 --qc-boxplots
134 #end if
135 #if str( $options.qcBarplots ) == "True"
136 --qc-barplots
137 #end if
138 #if str( $options.qcSnpHeatmap ) == "True"
139 --qc-snp-heatmap
140 #end if
141 #if str( $options.qcSnpHeatmap ) == "True"
142 --qc-snp-heatmap
143 #end if
144 #if str( $options.qcSnpBoxplot ) == "True"
145 --qc-snp-boxplot
146 #end if
147 #if str( $options.qcSnpBarplot ) == "True"
148 --qc-snp-barplot
149 #end if
150 #if str( $options.qcSampleBatchSize ) != ""
151 --qc-sample-batch-size="$options.qcSampleBatchSize"
152 #end if
153 #if str( $options.filteringContextRemoval ) != ""
154 --filtering-context-removal="$options.filteringContextRemoval"
155 #end if
156 #if str( $options.filteringSnp ) == "True"
157 --filtering-snp
158 #end if
159 #if str( $options.filteringSnpFrequency ) != ""
160 --filtering-snp-frequency="$options.filteringSnpFrequency"
161 #end if
162 #if str( $options.filteringSnpAccepted ) != ""
163 --filtering-snp-accepted="$options.filteringSnpAccepted"
164 #end if
165 #if str( $options.filteringSexChromosomesRemoval ) == "True"
166 --filtering-sex-chromosomes-removal
167 #end if
168 #if str( $options.filteringMissingValueQuantile ) != ""
169 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
170 #end if
171 #if str( $options.filteringCoverageThreshold ) != ""
172 --filtering-coverage-threshold="$options.filteringCoverageThreshold"
173 #end if
174 #if str( $options.filteringLowCoverageMasking ) == "True"
175 --filtering-low-coverage-masking
176 #end if
177 #if str( $options.filteringHighCoverageOutliers ) == "True"
178 --filtering-high-coverage-outliers
179 #end if
180 #if str( $options.filteringGreedycut ) == "True"
181 --filtering-greedycut
182 #end if
183 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
184 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
185 #end if
186 #if str( $options.filteringGreedycutRcTies ) != ""
187 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
188 #end if
189 #if str( $options.filteringDeviationThreshold ) != ""
190 --filtering-deviation-threshold="$options.filteringDeviationThreshold"
191 #end if
192 #if str( $options.batch ) == "True"
193 --batch
194 #end if
195 #if str( $options.batchDreductionColumns ) != ""
196 --batch-dreduction-columns="$options.batchDreductionColumns"
197 #end if
198 #if str( $options.batchPrincipalComponents ) != ""
199 --batch-principal-components="$options.batchPrincipalComponents"
200 #end if
201 #if str( $options.batchCorrelationColumns ) != ""
202 --batch-correlation-columns="$options.batchCorrelationColumns"
203 #end if
204 #if str( $options.batchCorrelationPvalueThreshold ) != ""
205 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold"
206 #end if
207 #if str( $options.batchCorrelationPermutations ) != ""
208 --batch-correlation-permutations="$options.batchCorrelationPermutations"
209 #end if
210 #if str( $options.batchCorrelationQc ) == "True"
211 --batch-correlation-qc
212 #end if
213 #if str( $options.profiles ) == "True"
214 --profiles
215 #end if
216 #if str( $options.profilesBetaDistribution ) == "True"
217 --profiles-beta-distribution
218 #end if
219 #if str( $options.profilesIntersample ) == "True"
220 --profiles-intersample
221 #end if
222 #if str( $options.profilesDeviationPlots ) == "True"
223 --profiles-deviation-plots
224 #end if
225 #if str( $options.profilesColumns ) != ""
226 --profiles-columns="$options.profilesColumns"
227 #end if
228 #if str( $options.profilesClustering ) == "True"
229 --profiles-clustering
230 #end if
231 #if str( $options.profilesClusteringTopProbes ) != ""
232 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes"
233 #end if
234 #if str( $options.regionProfilesTypes ) != ""
235 --region-profiles-types="$options.regionProfilesTypes"
236 #end if
237 #if str( $options.differential ) == "True"
238 --differential
239 #end if
240 #if str( $options.differentialPermutations ) != ""
241 --differential-permutations="$options.differentialPermutations"
242 #end if
243 #if str( $options.differentialComparisonColumns ) != ""
244 --differential-comparison-columns="$options.differentialComparisonColumns"
245 #end if
246 #if str( $options.differentialComparisonColumnsAllPairwise ) != ""
247 --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise"
248 #end if
249 #if str( $options.differentialEnrichment ) == "True"
250 --differential-enrichment
251 #end if
252 #if str( $options.exportToUcsc ) != ""
253 --export-to-ucsc="$options.exportToUcsc"
254 #end if
255 #if str( $options.exportToBed ) == "True"
256 --export-to-bed
257 #end if
258 #if str( $options.exportToCsv ) == "True"
259 --export-to-csv
260 #end if
261 #if str( $options.exportTypes ) != ""
262 --export-types="$options.exportTypes"
263 #end if
264 #if str( $options.colors3Gradient ) != ""
265 --colors-3-gradient="$options.colors3Gradient"
266 #end if
267 #if str( $options.loggingMemory ) == "True"
268 --logging-memory
269 #end if
270 #end if
271 </command>
272 <inputs>
273 <conditional name="inputDataSelector">
274 <param name="dataType" type="select" label="Data Type">
275 <option value="tables">Tabular data</option>
276 <option value="idats">IDAT files</option>
277 <option value="gsreport">GenomeStudio report</option>
278 <option value="geo">Gene Expression Omnibus series</option>
279 <option value="bed">BED files</option>
280 </param>
281 <when value="tables">
282 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
283 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
284 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
285 </when>
286 <when value="idats">
287 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
288 <conditional name="idatSelector">
289 <param name="idatSource" type="select" label="IDAT source">
290 <option value="history">Select from history</option>
291 <option value="repo">Repository on the server</option>
292 </param>
293 <when value="repo">
294 <param name="idatRepo" type="select" label="Select an IDAT repository">
295 <options from_data_table="rnbeads_repos">
296 <filter type="sort_by" column="2" />
297 <validator type="no_options" message="No repositories are available" />
298 </options>
299 </param>
300 </when>
301 <when value="history">
302 <repeat min="1" name="idatSeries" title="Input IDAT file">
303 <param name="idatFile" type="data" format="idat" label="IDAT file"/>
304 </repeat>
305 </when>
306 </conditional>
307 </when>
308 <when value="gsreport">
309 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
310 </when>
311 <when value="geo">
312 <param name="geoSeries" type="text" label="GEO series" />
313 </when>
314 <when value="bed">
315 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
316 <repeat min="1" name="bedSeries" title="Input BED file">
317 <param name="bedFile" type="data" format="bed" label="BED file"/>
318 </repeat>
319 </when>
320 </conditional>
321 <conditional name="options">
322 <param name="optionSet" type="select" label="Options Set">
323 <option value="default">Default options</option>
324 <option value="full">Full option set</option>
325 </param>
326 <when value="default" />
327 <when value="full">
328 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
329 <param name="logging" type="select" label="logging, logical" value="1">
330 <option value="True">True</option>
331 <option value="False">False</option>
332 </param>
333 <param name="email" type="text" label="email, character" value=""/>
334 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
335 <param name="columnsPairing" type="text" label="columns.pairing, integer vector" value=""/>
336 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
337 <option value="True">True</option>
338 <option value="False">False</option>
339 </param>
340 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
341 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
342 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
343 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
344 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
345 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
346 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
347 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
348 <option value="True">True</option>
349 <option value="False">False</option>
350 </param>
351 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
352 <option value="True">True</option>
353 <option value="False">False</option>
354 </param>
355 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
356 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
357 <option value="True">True</option>
358 <option value="False">False</option>
359 </param>
360 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
361 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/>
362 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
363 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
364 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
365 <param name="normalizationMethod" type="text" label="normalization.method, character" value="swan"/>
366 <param name="normalizationBackgroundMethod" type="text" label="normalization.background.method, character" value="methylumi.noob"/>
367 <param name="qc" type="select" label="qc, logical" value="1">
368 <option value="True">True</option>
369 <option value="False">False</option>
370 </param>
371 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
372 <option value="True">True</option>
373 <option value="False">False</option>
374 </param>
375 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
376 <option value="True">True</option>
377 <option value="False">False</option>
378 </param>
379 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
380 <option value="True">True</option>
381 <option value="False">False</option>
382 </param>
383 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
384 <option value="True">True</option>
385 <option value="False">False</option>
386 </param>
387 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
388 <option value="True">True</option>
389 <option value="False">False</option>
390 </param>
391 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
392 <option value="True">True</option>
393 <option value="False">False</option>
394 </param>
395 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="500"/>
396 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
397 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
398 <option value="True">True</option>
399 <option value="False">False</option>
400 </param>
401 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
402 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
403 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
404 <option value="True">True</option>
405 <option value="False">False</option>
406 </param>
407 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
408 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
409 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
410 <option value="True">True</option>
411 <option value="False">False</option>
412 </param>
413 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
414 <option value="True">True</option>
415 <option value="False">False</option>
416 </param>
417 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
418 <option value="True">True</option>
419 <option value="False">False</option>
420 </param>
421 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
422 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
423 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
424 <param name="batch" type="select" label="batch, logical" value="1">
425 <option value="True">True</option>
426 <option value="False">False</option>
427 </param>
428 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
429 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
430 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
431 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
432 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
433 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
434 <option value="True">True</option>
435 <option value="False">False</option>
436 </param>
437 <param name="profiles" type="select" label="profiles, logical" value="1">
438 <option value="True">True</option>
439 <option value="False">False</option>
440 </param>
441 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
442 <option value="True">True</option>
443 <option value="False">False</option>
444 </param>
445 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
446 <option value="True">True</option>
447 <option value="False">False</option>
448 </param>
449 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
450 <option value="True">True</option>
451 <option value="False">False</option>
452 </param>
453 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
454 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
455 <option value="True">True</option>
456 <option value="False">False</option>
457 </param>
458 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
459 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
460 <param name="differential" type="select" label="differential, logical" value="1">
461 <option value="True">True</option>
462 <option value="False">False</option>
463 </param>
464 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
465 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
466 <param name="differentialComparisonColumnsAllPairwise" type="text" label="differential.comparison.columns.all.pairwise, integer vector" value=""/>
467 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
468 <option value="True">True</option>
469 <option value="False">False</option>
470 </param>
471 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
472 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
473 <option value="True">True</option>
474 <option value="False">False</option>
475 </param>
476 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
477 <option value="True">True</option>
478 <option value="False">False</option>
479 </param>
480 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
481 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
482 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
483 <option value="True">True</option>
484 <option value="False">False</option>
485 </param>
486 </when>
487 </conditional>
488 </inputs>
489
490 <outputs>
491 <data format="html" name="html_file" label="index.html" />
492 </outputs>
493
494 <!--
495 <tests>
496 <test>
497 <param name="input" value="fa_gc_content_input.fa"/>
498 <output name="out_file1" file="fa_gc_content_output.txt"/>
499 </test>
500 </tests> -->
501
502 <help>
503 RnBeads is an R-package for comprehensive analysis of Illumina Infinium HumanMethylation450 BeadChip data. It extends previous approaches for this type of data analysis by high throughput capabilities, as well as presenting results in a comprehensive, highly interpretable fashion.
504 </help>
505
506 </tool>