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comparison rnbeads.xml @ 3:c21f50b45559 draft

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author pavlo-lutsik
date Wed, 17 Apr 2013 07:56:00 -0400
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2:518e1715678e 3:c21f50b45559
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.files_path"
49 #if str( $options.optionSet ) == "full"
50 #if str( $options.analysisName ) != ""
51 --analysis-name = "$options.analysisName"
52 #end if
53 #if str( $options.logging ) == "True"
54 --logging
55 #end if
56 #if str( $options.email ) != ""
57 --email = "$options.email"
58 #end if
59 #if str( $options.assembly ) != ""
60 --assembly = "$options.assembly"
61 #end if
62 #if str( $options.analyzeSites ) == "True"
63 --analyze-sites
64 #end if
65 #if str( $options.regionTypes ) != ""
66 --region-types = "$options.regionTypes"
67 #end if
68 #if str( $options.identifiersColumn ) != ""
69 --identifiers-column = "$options.identifiersColumn"
70 #end if
71 #if str( $options.pointsCategory ) != ""
72 --points-category = "$options.pointsCategory"
73 #end if
74 #if str( $options.colorsCategory ) != ""
75 --colors-category = "$options.colorsCategory"
76 #end if
77 #if str( $options.colorsGradient ) != ""
78 --colors-gradient = "$options.colorsGradient"
79 #end if
80 #if str( $options.minGroupSize ) != ""
81 --min-group-size = "$options.minGroupSize"
82 #end if
83 #if str( $options.maxGroupCount ) != ""
84 --max-group-count = "$options.maxGroupCount"
85 #end if
86 #if str( $options.gzLargeFiles ) == "True"
87 --gz-large-files
88 #end if
89 #if str( $options.strandSpecific ) == "True"
90 --strand-specific
91 #end if
92 #if str( $options.replicateIdColumn ) != ""
93 --replicate-id-column = "$options.replicateIdColumn"
94 #end if
95 #if str( $options.loadingNormalization ) == "True"
96 --loading-normalization
97 #end if
98 #if str( $options.loadingDefaultDataType ) != ""
99 --loading-default-data-type = "$options.loadingDefaultDataType"
100 #end if
101 #if str( $options.loadingTableSeparator ) != ""
102 --loading-table-separator = "$options.loadingTableSeparator"
103 #end if
104 #if str( $options.loadingBedStyle ) != ""
105 --loading-bed-style = "$options.loadingBedStyle"
106 #end if
107 #if str( $options.loadingBedColumns ) != ""
108 --loading-bed-columns = "$options.loadingBedColumns"
109 #end if
110 #if str( $options.loadingBedFrameShift ) != ""
111 --loading-bed-frame-shift = "$options.loadingBedFrameShift"
112 #end if
113 #if str( $options.normalizationMethod ) != ""
114 --normalization-method = "$options.normalizationMethod"
115 #end if
116 #if str( $options.qc ) == "True"
117 --qc
118 #end if
119 #if str( $options.qcBoxplots ) == "True"
120 --qc-boxplots
121 #end if
122 #if str( $options.qcBarplots ) == "True"
123 --qc-barplots
124 #end if
125 #if str( $options.qcNegativeBoxplot ) == "True"
126 --qc-negative-boxplot
127 #end if
128 #if str( $options.qcSnpHeatmap ) == "True"
129 --qc-snp-heatmap
130 #end if
131 #if str( $options.qcSnpBoxplot ) == "True"
132 --qc-snp-boxplot
133 #end if
134 #if str( $options.qcSnpBarplot ) == "True"
135 --qc-snp-barplot
136 #end if
137 #if str( $options.qcSampleBatchSize ) != ""
138 --qc-sample-batch-size = "$options.qcSampleBatchSize"
139 #end if
140 #if str( $options.filteringContextRemoval ) != ""
141 --filtering-context-removal = "$options.filteringContextRemoval"
142 #end if
143 #if str( $options.filteringSnp ) == "True"
144 --filtering-snp
145 #end if
146 #if str( $options.filteringSnpFrequency ) != ""
147 --filtering-snp-frequency = "$options.filteringSnpFrequency"
148 #end if
149 #if str( $options.filteringSnpAccepted ) != ""
150 --filtering-snp-accepted = "$options.filteringSnpAccepted"
151 #end if
152 #if str( $options.filteringSexChromosomesRemoval ) == "True"
153 --filtering-sex-chromosomes-removal
154 #end if
155 #if str( $options.filteringMissingValueQuantile ) != ""
156 --filtering-missing-value-quantile = "$options.filteringMissingValueQuantile"
157 #end if
158 #if str( $options.filteringCoverageThreshold ) != ""
159 --filtering-coverage-threshold = "$options.filteringCoverageThreshold"
160 #end if
161 #if str( $options.filteringLowCoverageMasking ) == "True"
162 --filtering-low-coverage-masking
163 #end if
164 #if str( $options.filteringHighCoverageOutliers ) == "True"
165 --filtering-high-coverage-outliers
166 #end if
167 #if str( $options.filteringGreedycut ) == "True"
168 --filtering-greedycut
169 #end if
170 #if str( $options.filteringGreedycutPvalueThreshold ) != ""
171 --filtering-greedycut-pvalue-threshold = "$options.filteringGreedycutPvalueThreshold"
172 #end if
173 #if str( $options.filteringGreedycutRcTies ) != ""
174 --filtering-greedycut-rc-ties = "$options.filteringGreedycutRcTies"
175 #end if
176 #if str( $options.filteringDeviationThreshold ) != ""
177 --filtering-deviation-threshold = "$options.filteringDeviationThreshold"
178 #end if
179 #if str( $options.batch ) == "True"
180 --batch
181 #end if
182 #if str( $options.batchDreductionColumns ) != ""
183 --batch-dreduction-columns = "$options.batchDreductionColumns"
184 #end if
185 #if str( $options.batchPrincipalComponents ) != ""
186 --batch-principal-components = "$options.batchPrincipalComponents"
187 #end if
188 #if str( $options.batchCorrelationColumns ) != ""
189 --batch-correlation-columns = "$options.batchCorrelationColumns"
190 #end if
191 #if str( $options.batchCorrelationPvalueThreshold ) != ""
192 --batch-correlation-pvalue-threshold = "$options.batchCorrelationPvalueThreshold"
193 #end if
194 #if str( $options.batchCorrelationPermutations ) != ""
195 --batch-correlation-permutations = "$options.batchCorrelationPermutations"
196 #end if
197 #if str( $options.batchCorrelationQc ) == "True"
198 --batch-correlation-qc
199 #end if
200 #if str( $options.profiles ) == "True"
201 --profiles
202 #end if
203 #if str( $options.profilesBetaDistribution ) == "True"
204 --profiles-beta-distribution
205 #end if
206 #if str( $options.profilesIntersample ) == "True"
207 --profiles-intersample
208 #end if
209 #if str( $options.profilesDeviationPlots ) == "True"
210 --profiles-deviation-plots
211 #end if
212 #if str( $options.profilesColumns ) != ""
213 --profiles-columns = "$options.profilesColumns"
214 #end if
215 #if str( $options.profilesClustering ) == "True"
216 --profiles-clustering
217 #end if
218 #if str( $options.profilesClusteringTopProbes ) != ""
219 --profiles-clustering-top-probes = "$options.profilesClusteringTopProbes"
220 #end if
221 #if str( $options.regionProfilesTypes ) != ""
222 --region-profiles-types = "$options.regionProfilesTypes"
223 #end if
224 #if str( $options.differential ) == "True"
225 --differential
226 #end if
227 #if str( $options.differentialPermutations ) != ""
228 --differential-permutations = "$options.differentialPermutations"
229 #end if
230 #if str( $options.differentialComparisonColumns ) != ""
231 --differential-comparison-columns = "$options.differentialComparisonColumns"
232 #end if
233 #if str( $options.differentialEnrichment ) == "True"
234 --differential-enrichment
235 #end if
236 #if str( $options.exportToUcsc ) != ""
237 --export-to-ucsc = "$options.exportToUcsc"
238 #end if
239 #if str( $options.exportToBed ) == "True"
240 --export-to-bed
241 #end if
242 #if str( $options.exportToCsv ) == "True"
243 --export-to-csv
244 #end if
245 #if str( $options.exportTypes ) != ""
246 --export-types = "$options.exportTypes"
247 #end if
248 #if str( $options.colors3Gradient ) != ""
249 --colors-3-gradient = "$options.colors3Gradient"
250 #end if
251 #if str( $options.loggingMemory ) == "True"
252 --logging-memory
253 #end if
254 #if str( $options.usePstoimg ) == "True"
255 --use-pstoimg
256 #end if
257 #end if
258 </command>
259 <inputs>
260 <conditional name="inputDataSelector">
261 <param name="dataType" type="select" label="Data Type">
262 <option value="tables">Tabular data</option>
263 <option value="idats">IDAT files</option>
264 <option value="gsreport">GenomeStudio report</option>
265 <option value="geo">Gene Expression Omnibus series</option>
266 <option value="bed">BED files</option>
267 </param>
268 <when value="tables">
269 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
270 <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/>
271 <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/>
272 </when>
273 <when value="idats">
274 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/>
275 <conditional name="idatSelector">
276 <param name="idatSource" type="select" label="IDAT source">
277 <option value="history">Select from history</option>
278 <option value="repo">Repository on the server</option>
279 </param>
280 <when value="repo">
281 <param name="idatRepo" type="select" label="Select an IDAT repository">
282 <options from_data_table="rnbeads_repos">
283 <filter type="sort_by" column="2" />
284 <validator type="no_options" message="No repositories are available" />
285 </options>
286 </param>
287 </when>
288 <when value="history">
289 <repeat min="1" name="idatSeries" title="Input IDAT file">
290 <param name="idatFiles" type="data" format="idat" label="IDAT file"/>
291 </repeat>
292 </when>
293 </conditional>
294 </when>
295 <when value="gsreport">
296 <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" />
297 </when>
298 <when value="geo">
299 <param name="geoSeries" type="text" label="GEO series" />
300 </when>
301 <when value="bed">
302 <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" />
303 <repeat min="1" name="bedSeries" title="Input BED file">
304 <param name="idatFiles" type="data" format="idat"/>
305 </repeat>
306 </when>
307 </conditional>
308 <conditional name="options">
309 <param name="optionSet" type="select" label="Options Set">
310 <option value="default">Default options</option>
311 <option value="full">Full option set</option>
312 </param>
313 <when value="default" />
314 <when value="full">
315 <label>See package documentation for detailed description of each option</label>
316 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
317 <param name="logging" type="select" label="logging, logical" value="1">
318 <option value="True">True</option>
319 <option value="False">False</option>
320 </param>
321 <param name="email" type="text" label="email, character" value=""/>
322 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
323 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
324 <option value="True">True</option>
325 <option value="False">False</option>
326 </param>
327 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
328 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
329 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
330 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
331 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
332 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
333 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
334 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
335 <option value="True">True</option>
336 <option value="False">False</option>
337 </param>
338 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
339 <option value="True">True</option>
340 <option value="False">False</option>
341 </param>
342 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
343 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
344 <option value="True">True</option>
345 <option value="False">False</option>
346 </param>
347 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
348 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/>
349 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
350 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
351 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
352 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/>
353 <param name="qc" type="select" label="qc, logical" value="1">
354 <option value="True">True</option>
355 <option value="False">False</option>
356 </param>
357 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
358 <option value="True">True</option>
359 <option value="False">False</option>
360 </param>
361 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
362 <option value="True">True</option>
363 <option value="False">False</option>
364 </param>
365 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
366 <option value="True">True</option>
367 <option value="False">False</option>
368 </param>
369 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
370 <option value="True">True</option>
371 <option value="False">False</option>
372 </param>
373 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
374 <option value="True">True</option>
375 <option value="False">False</option>
376 </param>
377 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
378 <option value="True">True</option>
379 <option value="False">False</option>
380 </param>
381 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/>
382 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
383 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
384 <option value="True">True</option>
385 <option value="False">False</option>
386 </param>
387 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
388 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
389 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
390 <option value="True">True</option>
391 <option value="False">False</option>
392 </param>
393 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
394 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
395 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
396 <option value="True">True</option>
397 <option value="False">False</option>
398 </param>
399 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
400 <option value="True">True</option>
401 <option value="False">False</option>
402 </param>
403 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
404 <option value="True">True</option>
405 <option value="False">False</option>
406 </param>
407 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
408 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
409 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
410 <param name="batch" type="select" label="batch, logical" value="1">
411 <option value="True">True</option>
412 <option value="False">False</option>
413 </param>
414 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
415 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
416 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
417 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
418 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
419 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
420 <option value="True">True</option>
421 <option value="False">False</option>
422 </param>
423 <param name="profiles" type="select" label="profiles, logical" value="1">
424 <option value="True">True</option>
425 <option value="False">False</option>
426 </param>
427 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
428 <option value="True">True</option>
429 <option value="False">False</option>
430 </param>
431 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
432 <option value="True">True</option>
433 <option value="False">False</option>
434 </param>
435 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
436 <option value="True">True</option>
437 <option value="False">False</option>
438 </param>
439 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
440 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
441 <option value="True">True</option>
442 <option value="False">False</option>
443 </param>
444 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
445 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
446 <param name="differential" type="select" label="differential, logical" value="1">
447 <option value="True">True</option>
448 <option value="False">False</option>
449 </param>
450 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
451 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
452 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
453 <option value="True">True</option>
454 <option value="False">False</option>
455 </param>
456 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
457 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
458 <option value="True">True</option>
459 <option value="False">False</option>
460 </param>
461 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
462 <option value="True">True</option>
463 <option value="False">False</option>
464 </param>
465 <param name="exportTypes" type="text" label="export.types, character vector" value=""/>
466 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
467 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
468 <option value="True">True</option>
469 <option value="False">False</option>
470 </param>
471 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
472 <option value="True">True</option>
473 <option value="False">False</option>
474 </param>
475 </when>
476 </conditional>
477 </inputs>
478
479 <outputs>
480 <data format="html" name="html_file" label="index.html" />
481 </outputs>
482
483 <!--
484 <tests>
485 <test>
486 <param name="input" value="fa_gc_content_input.fa"/>
487 <output name="out_file1" file="fa_gc_content_output.txt"/>
488 </test>
489 </tests> -->
490
491 <help>
492 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.
493 </help>
494
495 </tool>