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comparison variant_annotator.xml @ 11:432aafa6830a draft

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author david-hoover
date Wed, 12 Sep 2012 17:54:46 -0400
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10:b138c5569231 11:432aafa6830a
1 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.1">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="2.1">gatk</requirement>
5 <requirement type="package">samtools</requirement>
6 </requirements>
7 <command interpreter="python">gatk2_wrapper.py
8 --max_jvm_heap_fraction "1"
9 --stdout "${output_log}"
10 #if str( $reference_source.input_bam ) != "None":
11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
14 #end if
15 #end if
16 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
17 -p 'java
18 -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar"
19 ##--list
20 -T "VariantAnnotator"
21 ##--num_threads 4 ##hard coded, for now
22 -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home
23 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
24 #if $reference_source.reference_source_selector != "history":
25 -R "${reference_source.ref_file.fields.path}"
26 #end if
27 -o "${output_vcf}"
28 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
29 --useAllAnnotations
30 #else:
31 #if $annotations_type.annotations:
32 #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ):
33 --annotation "${annotation}"
34 #end for
35 #end if
36 #end if
37 #if $exclude_annotations:
38 #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ):
39 --excludeAnnotation "${annotation}"
40 #end for
41 #end if
42 #for $additional_annotation in $additional_annotations:
43 --annotation "${additional_annotation.additional_annotation_name}"
44 #end for
45 '
46 #if $reference_source.input_variant_bti:
47 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
48 #end if
49
50 #for $rod_binding in $comp_rod_bind:
51 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
52 #end for
53
54 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
55 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
56 #end if
57
58
59 #for $rod_binding in $resource_rod_bind:
60 -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
61 #end for
62
63 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
64 -p '--annotation "SnpEff"'
65 -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
66 #else:
67 -p '--excludeAnnotation "SnpEff"'
68 #end if
69
70 #for $expression in $expressions:
71 -p '--expression "${expression.expression}"'
72 #end for
73
74 ##start standard gatk options
75 #if $gatk_param_type.gatk_param_type_selector == "advanced":
76 #for $pedigree in $gatk_param_type.pedigree:
77 -p '--pedigree "${pedigree.pedigree_file}"'
78 #end for
79 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
80 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
81 #end for
82 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
83 #for $read_filter in $gatk_param_type.read_filter:
84 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
85 ###raise Exception( str( dir( $read_filter ) ) )
86 #for $name, $param in $read_filter.read_filter_type.iteritems():
87 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
88 #if hasattr( $param.input, 'truevalue' ):
89 ${param}
90 #else:
91 --${name} "${param}"
92 #end if
93 #end if
94 #end for
95 '
96 #end for
97 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
98 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
99 #end for
100
101 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
102 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
103 #end for
104
105 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
106
107 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
108 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
109 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
110 #end if
111 -p '
112 --baq "${gatk_param_type.baq}"
113 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
114 ${gatk_param_type.use_original_qualities}
115 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
116 --validation_strictness "${gatk_param_type.validation_strictness}"
117 --interval_merging "${gatk_param_type.interval_merging}"
118 ${gatk_param_type.disable_experimental_low_memory_sharding}
119 ${gatk_param_type.non_deterministic_random_seed}
120 '
121 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
122 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
123 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
124 #else
125 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
126 #end if
127 #end for
128 #end if
129 #if str( $reference_source.reference_source_selector ) == "history":
130 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
131 #end if
132 ##end standard gatk options
133
134 -p '
135 #if str( $annotation_group ) != "None":
136 #for $group in str( $annotation_group ).split( ',' ):
137 --group "${group}"
138 #end for
139 #end if
140 #if str( $family_string ) != "":
141 --family_string "${family_string}"
142 #end if
143 --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}"
144 '
145 </command>
146 <inputs>
147 <conditional name="reference_source">
148 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
149 <option value="cached">Locally cached</option>
150 <option value="history">History</option>
151 </param>
152 <when value="cached">
153 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
154 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
155 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
156 <validator type="unspecified_build" />
157 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
158 </param>
159 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
160 <options from_data_table="gatk2_picard_indexes">
161 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
162 </options>
163 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
164 </param>
165 </when>
166 <when value="history"> <!-- FIX ME!!!! -->
167 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
168 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
169 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
170 </param>
171 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
172 </when>
173 </conditional>
174 <conditional name="annotations_type">
175 <param name="annotations_type_selector" type="select" label="Use all possible annotations">
176 <option value="use_all_annotations">Use all</option>
177 <option value="choose" selected="True">Use selected</option>
178 </param>
179 <when value="use_all_annotations">
180 <!-- no extra options here -->
181 </when>
182 <when value="choose">
183 <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &amp;lt;annotation&amp;gt;" >
184 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
185 <options from_data_table="gatk2_annotations">
186 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
187 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
188 </options>
189 </param>
190 </when>
191 </conditional>
192
193 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
194 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
195 </repeat>
196
197 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
198 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
199 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
200 </repeat>
201
202 <conditional name="dbsnp_rod_bind_type">
203 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
204 <option value="set_dbsnp" selected="True">Set dbSNP</option>
205 <option value="exclude_dbsnp">Don't set dbSNP</option>
206 </param>
207 <when value="exclude_dbsnp">
208 <!-- Do nothing here -->
209 </when>
210 <when value="set_dbsnp">
211 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
212 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
213 </when>
214 </conditional>
215
216 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
217 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
218 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
219 </repeat>
220
221 <conditional name="snpEff_rod_bind_type">
222 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
223 <option value="set_snpEff">Set snpEff</option>
224 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
225 </param>
226 <when value="exclude_snpEff">
227 <!-- Do nothing here -->
228 </when>
229 <when value="set_snpEff">
230 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
231 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
232 </when>
233 </conditional>
234
235 <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
236 <param name="expression" type="text" value="" label="Expression"/>
237 </repeat>
238
239 <conditional name="gatk_param_type">
240 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
241 <option value="basic" selected="True">Basic</option>
242 <option value="advanced">Advanced</option>
243 </param>
244 <when value="basic">
245 <!-- Do nothing here -->
246 </when>
247 <when value="advanced">
248 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
249 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
250 </repeat>
251 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
252 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
253 </repeat>
254 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
255 <option value="STRICT" selected="True">STRICT</option>
256 <option value="SILENT">SILENT</option>
257 </param>
258 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
259 <conditional name="read_filter_type">
260 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
261 <option value="BadCigar">BadCigar</option>
262 <option value="BadMate">BadMate</option>
263 <option value="DuplicateRead">DuplicateRead</option>
264 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
265 <option value="MalformedRead">MalformedRead</option>
266 <option value="MappingQuality">MappingQuality</option>
267 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
268 <option value="MappingQualityZero">MappingQualityZero</option>
269 <option value="MateSameStrand">MateSameStrand</option>
270 <option value="MaxInsertSize">MaxInsertSize</option>
271 <option value="MaxReadLength" selected="True">MaxReadLength</option>
272 <option value="MissingReadGroup">MissingReadGroup</option>
273 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
274 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
275 <option value="Platform454">Platform454</option>
276 <option value="Platform">Platform</option>
277 <option value="PlatformUnit">PlatformUnit</option>
278 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
279 <option value="ReadName">ReadName</option>
280 <option value="ReadStrand">ReadStrand</option>
281 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
282 <option value="Sample">Sample</option>
283 <option value="SingleReadGroup">SingleReadGroup</option>
284 <option value="UnmappedRead">UnmappedRead</option>
285 </param>
286 <when value="BadCigar">
287 <!-- no extra options -->
288 </when>
289 <when value="BadMate">
290 <!-- no extra options -->
291 </when>
292 <when value="DuplicateRead">
293 <!-- no extra options -->
294 </when>
295 <when value="FailsVendorQualityCheck">
296 <!-- no extra options -->
297 </when>
298 <when value="MalformedRead">
299 <!-- no extra options -->
300 </when>
301 <when value="MappingQuality">
302 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
303 </when>
304 <when value="MappingQualityUnavailable">
305 <!-- no extra options -->
306 </when>
307 <when value="MappingQualityZero">
308 <!-- no extra options -->
309 </when>
310 <when value="MateSameStrand">
311 <!-- no extra options -->
312 </when>
313 <when value="MaxInsertSize">
314 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
315 </when>
316 <when value="MaxReadLength">
317 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
318 </when>
319 <when value="MissingReadGroup">
320 <!-- no extra options -->
321 </when>
322 <when value="NoOriginalQualityScores">
323 <!-- no extra options -->
324 </when>
325 <when value="NotPrimaryAlignment">
326 <!-- no extra options -->
327 </when>
328 <when value="Platform454">
329 <!-- no extra options -->
330 </when>
331 <when value="Platform">
332 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
333 </when>
334 <when value="PlatformUnit">
335 <!-- no extra options -->
336 </when>
337 <when value="ReadGroupBlackList">
338 <!-- no extra options -->
339 </when>
340 <when value="ReadName">
341 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
342 </when>
343 <when value="ReadStrand">
344 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
345 </when>
346 <when value="ReassignMappingQuality">
347 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
348 </when>
349 <when value="Sample">
350 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
351 </when>
352 <when value="SingleReadGroup">
353 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
354 </when>
355 <when value="UnmappedRead">
356 <!-- no extra options -->
357 </when>
358 </conditional>
359 </repeat>
360 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
361 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
362 </repeat>
363 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
364 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
365 </repeat>
366
367 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
368 <option value="UNION" selected="True">UNION</option>
369 <option value="INTERSECTION">INTERSECTION</option>
370 </param>
371
372 <conditional name="downsampling_type">
373 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
374 <option value="NONE" selected="True">NONE</option>
375 <option value="ALL_READS">ALL_READS</option>
376 <option value="BY_SAMPLE">BY_SAMPLE</option>
377 </param>
378 <when value="NONE">
379 <!-- no more options here -->
380 </when>
381 <when value="ALL_READS">
382 <conditional name="downsample_to_type">
383 <param name="downsample_to_type_selector" type="select" label="Downsample method">
384 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
385 <option value="downsample_to_coverage">Downsample by Coverage</option>
386 </param>
387 <when value="downsample_to_fraction">
388 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
389 </when>
390 <when value="downsample_to_coverage">
391 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
392 </when>
393 </conditional>
394 </when>
395 <when value="BY_SAMPLE">
396 <conditional name="downsample_to_type">
397 <param name="downsample_to_type_selector" type="select" label="Downsample method">
398 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
399 <option value="downsample_to_coverage">Downsample by Coverage</option>
400 </param>
401 <when value="downsample_to_fraction">
402 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
403 </when>
404 <when value="downsample_to_coverage">
405 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
406 </when>
407 </conditional>
408 </when>
409 </conditional>
410 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
411 <option value="OFF" selected="True">OFF</option>
412 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
413 <option value="RECALCULATE">RECALCULATE</option>
414 </param>
415 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
416 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
417 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
418 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
419 <option value="STRICT" selected="True">STRICT</option>
420 <option value="LENIENT">LENIENT</option>
421 <option value="SILENT">SILENT</option>
422 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
423 </param>
424 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
425 <option value="ALL" selected="True">ALL</option>
426 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
427 </param>
428
429 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
430 <conditional name="read_group_black_list_type">
431 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
432 <option value="file" selected="True">Filters in file</option>
433 <option value="text">Specify filters as a string</option>
434 </param>
435 <when value="file">
436 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
437 </when>
438 <when value="text">
439 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
440 </when>
441 </conditional>
442 </repeat>
443
444 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
445 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
446
447 </when>
448 </conditional>
449
450 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;">
451 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
452 <option value="Standard">Standard</option>
453 <option value="Experimental">Experimental</option>
454 <option value="WorkInProgress">WorkInProgress</option>
455 <option value="RankSumTest">RankSumTest</option>
456 </param>
457 <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
458 <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &amp;lt;MendelViolationGenotypeQualityThreshold&amp;gt;"/>
459 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
460 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
461 <options from_data_table="gatk_annotations">
462 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
463 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
464 </options>
465 </param>
466
467 </inputs>
468 <outputs>
469 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
470 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
471 </outputs>
472 <tests>
473 <test>
474 <param name="reference_source_selector" value="history" />
475 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
476 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
477 <param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" />
478 <param name="input_variant_bti" />
479 <param name="annotations_type_selector" value="choose" />
480 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
481 <param name="additional_annotations" value="0" />
482 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
483 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
484 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
485 <param name="gatk_param_type_selector" value="basic" />
486 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
487 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
488 <param name="comp_rod_bind" value="0" />
489 <param name="resource_rod_bind" value="0" />
490 <param name="expressions" value="0" />
491 <!-- <param name="annotation_group" /> -->
492 </test>
493 </tests>
494 <help>
495 **What it does**
496
497 Annotates variant calls with context information. Users can specify which of the available annotations to use.
498
499 For more information on using the VariantAnnotator, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator&gt;`_.
500
501 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
502
503 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
504
505 ------
506
507
508 **Inputs**
509
510 GenomeAnalysisTK: VariantAnnotator accepts a variant input file.
511
512
513 **Outputs**
514
515 The output is in VCF format.
516
517
518 Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
519
520 -------
521
522 **Settings**::
523
524
525 sampleName The sample (NA-ID) corresponding to the variant input (for non-VCF input only)
526 annotation One or more specific annotations to apply to variant calls
527 group One or more classes/groups of annotations to apply to variant calls
528 expression One or more specific expressions to apply to variant calls; see documentation for more details
529 useAllAnnotations Use all possible annotations (not for the faint of heart)
530
531 ------
532
533 **Citation**
534
535 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
536
537 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
538
539 </help>
540 </tool>