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comparison rnbeads.xml @ 11:ce411254e4a9 draft

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author pavlo-lutsik
date Sat, 20 Apr 2013 07:14:22 -0400
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10:945690943560 11:ce411254e4a9
1 <?xml version="0.9"?>
2 <tool id="rnbeads" name="RnBeads" version="0.9">
3 <description>Performs RnBeads analysis for the selected set of </description>
4 <requirements>
5 <requirement type="set_environment" version="0.9">R_SCRIPTS_PATH</requirement>
6 <requirement type="package" version="3.0.0">R</requirement>
7 </requirements>
8 <command interpreter="bash">rnbeads_galaxy_wrapper.sh
9 #if str( $inputDataSelector.dataType ) == "idat"
10 --data-type="idat.dir"
11 --pheno="$inputDataSelector.sampleAnnotations"
12 #if str( $idatSelector.idatSelector.idatSource ) == "history"
13 --idat-files =="
14 #for $input_files in $inputDataSelector.input_series:
15 ${input_files.input_files}\t
16 #end for
17 "
18 #else:
19 --idat-files == "$idatRepo"
20 #end if
21 #end if
22 #if str( $inputDataSelector.dataType ) == "gsreport"
23 --data-type="GS.report"
24 --gs-report="$inputDataSelector.gsReportFile"
25 #end if
26 #if str( $inputDataSelector.dataType ) == "geo"
27 --data-type="GEO"
28 --geo-series=$inputDataSelector.geoSeries
29 #end if
30 #if str( $inputDataSelector.dataType ) == "tables"
31 --data-type="data.files"
32 --pheno="$inputDataSelector.sampleAnnotations"
33 #end if
34 #if str( $inputDataSelector.dataType ) == "tables"
35 --data-type="data.files"
36 --pheno="$inputDataSelector.sampleAnnotations"
37 --betas="$inputDataSelector.betaTable"
38 --pvals="$inputDataSelector.pvalTable"
39 #end if
40 #if str( $inputDataSelector.dataType ) == "bed"
41 --data-type="bed.dir"
42 --pheno="$inputDataSelector.sampleAnnotations"
43 --beds =="
44 #for $input_files in $inputDataSelector.input_series:
45 ${input_files.input_files}\t
46 #end for
47 #end if
48 --report-dir="$html_file.extra_files_path"
49 --output-file="$html_file"
50 #if str( $options.optionSet ) == "full"
51 #if str( $options.analysisName ) != ""
52 --analysis-name="$options.analysisName"
53 #end if
54 #if str( $options.logging ) == "True"
55 --logging
56 #end if
57 #if str( $options.email ) != ""
58 --email="$options.email"
59 #end if
60 #if str( $options.assembly ) != ""
61 --assembly="$options.assembly"
62 #end if
63 #if str( $options.analyzeSites ) == "True"
64 --analyze-sites
65 #end if
66 #if str( $options.regionTypes ) != ""
67 --region-types="$options.regionTypes"
68 #end if
69 #if str( $options.identifiersColumn ) != ""
70 --identifiers-column="$options.identifiersColumn"
71 #end if
72 #if str( $options.pointsCategory ) != ""
73 --points-category="$options.pointsCategory"
74 #end if
75 #if str( $options.colorsCategory ) != ""
76 --colors-category="$options.colorsCategory"
77 #end if
78 #if str( $options.colorsGradient ) != ""
79 --colors-gradient="$options.colorsGradient"
80 #end if
81 #if str( $options.minGroupSize ) != ""
82 --min-group-size="$options.minGroupSize"
83 #end if
84 #if str( $options.maxGroupCount ) != ""
85 --max-group-count="$options.maxGroupCount"
86 #end if
87 #if str( $options.gzLargeFiles ) == "True"
88 --gz-large-files
89 #end if
90 #if str( $options.strandSpecific ) == "True"
91 --strand-specific
92 #end if
93 #if str( $options.replicateIdColumn ) != ""
94 --replicate-id-column="$options.replicateIdColumn"
95 #end if
96 #if str( $options.loadingNormalization ) == "True"
97 --loading-normalization
98 #end if
99 #if str( $options.loadingDefaultDataType ) != ""
100 --loading-default-data-type="$options.loadingDefaultDataType"
101 #end if
102 #if str( $options.loadingTableSeparator ) != ""
103 --loading-table-separator="$options.loadingTableSeparator"
104 #end if
105 #if str( $options.loadingBedStyle ) != ""
106 --loading-bed-style="$options.loadingBedStyle"
107 #end if
108 #if str( $options.loadingBedColumns ) != ""
109 --loading-bed-columns="$options.loadingBedColumns"
110 #end if
111 #if str( $options.loadingBedFrameShift ) != ""
112 --loading-bed-frame-shift="$options.loadingBedFrameShift"
113 #end if
114 #if str( $options.normalizationMethod ) != ""
115 --normalization-method="$options.normalizationMethod"
116 #end if
117 #if str( $options.normalizationSubtractBackground ) == "True"
118 --normalization-subtract-background
119 #end if
120 #if str( $options.qc ) == "True"
121 --qc
122 #end if
123 #if str( $options.qcBoxplots ) == "True"
124 --qc-boxplots
125 #end if
126 #if str( $options.qcBarplots ) == "True"
127 --qc-barplots
128 #end if
129 #if str( $options.qcNegativeBoxplot ) == "True"
130 --qc-negative-boxplot
131 #end if
132 #if str( $options.qcSnpHeatmap ) == "True"
133 --qc-snp-heatmap
134 #end if
135 #if str( $options.qcSnpBoxplot ) == "True"
136 --qc-snp-boxplot
137 #end if
138 #if str( $options.qcSnpBarplot ) == "True"
139 --qc-snp-barplot
140 #end if
141 #if str( $options.qcSampleBatchSize ) != ""
142 --qc-sample-batch-size="$options.qcSampleBatchSize"
143 #end if
144 #if str( $options.filteringContextRemoval ) != ""
145 --filtering-context-removal="$options.filteringContextRemoval"
146 #end if
147 #if str( $options.filteringSnp ) == "True"
148 --filtering-snp
149 #end if
150 #if str( $options.filteringSnpFrequency ) != ""
151 --filtering-snp-frequency="$options.filteringSnpFrequency"
152 #end if
153 #if str( $options.filteringSnpAccepted ) != ""
154 --filtering-snp-accepted="$options.filteringSnpAccepted"
155 #end if
156 #if str( $options.filteringSexChromosomesRemoval ) == "True"
157 --filtering-sex-chromosomes-removal
158 #end if
159 #if str( $options.filteringMissingValueQuantile ) != ""
160 --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
161 #end if
162 #if str( $options.filteringCoverageThreshold ) != ""
163 --filtering-coverage-threshold="$options.filteringCoverageThreshold"
164 #end if
165 #if str( $options.filteringLowCoverageMasking ) == "True"
166 --filtering-low-coverage-masking
167 #end if
168 #if str( $options.filteringHighCoverageOutliers ) == "True"
169 --filtering-high-coverage-outliers
170 #end if
171 #if str( $options.filteringGreedycut ) == "True"
172 --filtering-greedycut
173 #end if
174 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
175 --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
176 #end if
177 #if str( $options.filteringGreedycutRcTies ) != ""
178 --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
179 #end if
180 #if str( $options.filteringDeviationThreshold ) != ""
181 --filtering-deviation-threshold="$options.filteringDeviationThreshold"
182 #end if
183 #if str( $options.batch ) == "True"
184 --batch
185 #end if
186 #if str( $options.batchDreductionColumns ) != ""
187 --batch-dreduction-columns="$options.batchDreductionColumns"
188 #end if
189 #if str( $options.batchPrincipalComponents ) != ""
190 --batch-principal-components="$options.batchPrincipalComponents"
191 #end if
192 #if str( $options.batchCorrelationColumns ) != ""
193 --batch-correlation-columns="$options.batchCorrelationColumns"
194 #end if
195 #if str( $options.batchCorrelationPvalueThreshold ) != ""
196 --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold"
197 #end if
198 #if str( $options.batchCorrelationPermutations ) != ""
199 --batch-correlation-permutations="$options.batchCorrelationPermutations"
200 #end if
201 #if str( $options.batchCorrelationQc ) == "True"
202 --batch-correlation-qc
203 #end if
204 #if str( $options.profiles ) == "True"
205 --profiles
206 #end if
207 #if str( $options.profilesBetaDistribution ) == "True"
208 --profiles-beta-distribution
209 #end if
210 #if str( $options.profilesIntersample ) == "True"
211 --profiles-intersample
212 #end if
213 #if str( $options.profilesDeviationPlots ) == "True"
214 --profiles-deviation-plots
215 #end if
216 #if str( $options.profilesColumns ) != ""
217 --profiles-columns="$options.profilesColumns"
218 #end if
219 #if str( $options.profilesClustering ) == "True"
220 --profiles-clustering
221 #end if
222 #if str( $options.profilesClusteringTopProbes ) != ""
223 --profiles-clustering-top-probes="$options.profilesClusteringTopProbes"
224 #end if
225 #if str( $options.regionProfilesTypes ) != ""
226 --region-profiles-types="$options.regionProfilesTypes"
227 #end if
228 #if str( $options.differential ) == "True"
229 --differential
230 #end if
231 #if str( $options.differentialPermutations ) != ""
232 --differential-permutations="$options.differentialPermutations"
233 #end if
234 #if str( $options.differentialComparisonColumns ) != ""
235 --differential-comparison-columns="$options.differentialComparisonColumns"
236 #end if
237 #if str( $options.differentialEnrichment ) == "True"
238 --differential-enrichment
239 #end if
240 #if str( $options.exportToUcsc ) != ""
241 --export-to-ucsc="$options.exportToUcsc"
242 #end if
243 #if str( $options.exportToBed ) == "True"
244 --export-to-bed
245 #end if
246 #if str( $options.exportToCsv ) == "True"
247 --export-to-csv
248 #end if
249 #if str( $options.exportTypes ) != ""
250 --export-types="$options.exportTypes"
251 #end if
252 #if str( $options.colors3Gradient ) != ""
253 --colors-3-gradient="$options.colors3Gradient"
254 #end if
255 #if str( $options.loggingMemory ) == "True"
256 --logging-memory
257 #end if
258 #if str( $options.usePstoimg ) == "True"
259 --use-pstoimg
260 #end if
261 #end if
262 </command>
263 <inputs>
264 <conditional name="inputDataSelector">
265 <param name="dataType" type="select" label="Data Type">
266 <option value="tables">Tabular data</option>
267 <option value="idats">IDAT files</option>
268 <option value="gsreport">GenomeStudio report</option>
269 <option value="geo">Gene Expression Omnibus series</option>
270 <option value="bed">BED files</option>
271 </param>
272 <when value="tables">
273 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
274 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
275 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
276 </when>
277 <when value="idats">
278 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
279 <conditional name="idatSelector">
280 <param name="idatSource" type="select" label="IDAT source">
281 <option value="history">Select from history</option>
282 <option value="repo">Repository on the server</option>
283 </param>
284 <when value="repo">
285 <param name="idatRepo" type="select" label="Select an IDAT repository">
286 <options from_data_table="rnbeads_repos">
287 <filter type="sort_by" column="2" />
288 <validator type="no_options" message="No repositories are available" />
289 </options>
290 </param>
291 </when>
292 <when value="history">
293 <repeat min="1" name="idatSeries" title="Input IDAT file">
294 <param name="idatFiles" type="data" format="idat" label="IDAT file"/>
295 </repeat>
296 </when>
297 </conditional>
298 </when>
299 <when value="gsreport">
300 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
301 </when>
302 <when value="geo">
303 <param name="geoSeries" type="text" label="GEO series" />
304 </when>
305 <when value="bed">
306 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
307 <repeat min="1" name="bedSeries" title="Input BED file">
308 <param name="idatFiles" type="data" format="idat"/>
309 </repeat>
310 </when>
311 </conditional>
312 <conditional name="options">
313 <param name="optionSet" type="select" label="Options Set">
314 <option value="default">Default options</option>
315 <option value="full">Full option set</option>
316 </param>
317 <when value="default" />
318 <when value="full">
319 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
320 <param name="logging" type="select" label="logging, logical" value="1">
321 <option value="True">True</option>
322 <option value="False">False</option>
323 </param>
324 <param name="email" type="text" label="email, character" value=""/>
325 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
326 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
327 <option value="True">True</option>
328 <option value="False">False</option>
329 </param>
330 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
331 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
332 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
333 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
334 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
335 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
336 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
337 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
338 <option value="True">True</option>
339 <option value="False">False</option>
340 </param>
341 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
342 <option value="True">True</option>
343 <option value="False">False</option>
344 </param>
345 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
346 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
347 <option value="True">True</option>
348 <option value="False">False</option>
349 </param>
350 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
351 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/>
352 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
353 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
354 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
355 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/>
356 <param name="normalizationSubtractBackground" type="select" label="normalization.subtract.background, logical" value="0">
357 <option value="True">True</option>
358 <option value="False">False</option>
359 </param>
360 <param name="qc" type="select" label="qc, logical" value="1">
361 <option value="True">True</option>
362 <option value="False">False</option>
363 </param>
364 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
365 <option value="True">True</option>
366 <option value="False">False</option>
367 </param>
368 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
369 <option value="True">True</option>
370 <option value="False">False</option>
371 </param>
372 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
373 <option value="True">True</option>
374 <option value="False">False</option>
375 </param>
376 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
377 <option value="True">True</option>
378 <option value="False">False</option>
379 </param>
380 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
381 <option value="True">True</option>
382 <option value="False">False</option>
383 </param>
384 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
385 <option value="True">True</option>
386 <option value="False">False</option>
387 </param>
388 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/>
389 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
390 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
391 <option value="True">True</option>
392 <option value="False">False</option>
393 </param>
394 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
395 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
396 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
397 <option value="True">True</option>
398 <option value="False">False</option>
399 </param>
400 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
401 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
402 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
403 <option value="True">True</option>
404 <option value="False">False</option>
405 </param>
406 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
407 <option value="True">True</option>
408 <option value="False">False</option>
409 </param>
410 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
411 <option value="True">True</option>
412 <option value="False">False</option>
413 </param>
414 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
415 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
416 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
417 <param name="batch" type="select" label="batch, logical" value="1">
418 <option value="True">True</option>
419 <option value="False">False</option>
420 </param>
421 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
422 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
423 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
424 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
425 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
426 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
427 <option value="True">True</option>
428 <option value="False">False</option>
429 </param>
430 <param name="profiles" type="select" label="profiles, logical" value="1">
431 <option value="True">True</option>
432 <option value="False">False</option>
433 </param>
434 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
435 <option value="True">True</option>
436 <option value="False">False</option>
437 </param>
438 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
439 <option value="True">True</option>
440 <option value="False">False</option>
441 </param>
442 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
443 <option value="True">True</option>
444 <option value="False">False</option>
445 </param>
446 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
447 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
448 <option value="True">True</option>
449 <option value="False">False</option>
450 </param>
451 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
452 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
453 <param name="differential" type="select" label="differential, logical" value="1">
454 <option value="True">True</option>
455 <option value="False">False</option>
456 </param>
457 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
458 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
459 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
460 <option value="True">True</option>
461 <option value="False">False</option>
462 </param>
463 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
464 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
465 <option value="True">True</option>
466 <option value="False">False</option>
467 </param>
468 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
469 <option value="True">True</option>
470 <option value="False">False</option>
471 </param>
472 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
473 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
474 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
475 <option value="True">True</option>
476 <option value="False">False</option>
477 </param>
478 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
479 <option value="True">True</option>
480 <option value="False">False</option>
481 </param>
482 </when>
483 </conditional>
484 </inputs>
485
486 <outputs>
487 <data format="html" name="html_file" label="index.html" />
488 </outputs>
489
490 <!--
491 <tests>
492 <test>
493 <param name="input" value="fa_gc_content_input.fa"/>
494 <output name="out_file1" file="fa_gc_content_output.txt"/>
495 </test>
496 </tests> -->
497
498 <help>
499 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.
500 </help>
501
502 </tool>