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comparison base_recalibrator.xml @ 0:74c05070a3f8 draft

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author jjohnson
date Thu, 01 Nov 2012 13:53:22 -0400
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1 <tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.4">
2 <description>on BAM files</description>
3 <requirements>
4 <requirement type="package" version="2.2">gatk</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements>
7 <command interpreter="python">gatk2_wrapper.py
8 --max_jvm_heap_fraction "1"
9 --stdout "${output_log}"
10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
12 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
13 #end if
14 -p 'java
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
16 -T "BaseRecalibrator"
17 \$GATK2_SITE_OPTIONS
18 ##--num_threads 4 ##hard coded, for now
19 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
20 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
21 #if $reference_source.reference_source_selector != "history":
22 -R "${reference_source.ref_file.fields.path}"
23 #end if
24 --out "${output_recal}"
25 ${standard_covs}
26 #if str( $covariates ) != "None":
27 #for $cov in str( $covariates ).split( ',' ):
28 -cov "${cov}"
29 #end for
30 #end if
31 '
32
33 #set $snp_dataset_provided = False
34 #set $rod_binding_names = dict()
35 #for $rod_binding in $rod_bind:
36 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
37 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
38 #else
39 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
40 #end if
41 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'dbsnp':
42 #set $snp_dataset_provided = True
43 #end if
44 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
45 -d "--knownSites:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
46 #end for
47
48 ##start standard gatk options
49 #if $gatk_param_type.gatk_param_type_selector == "advanced":
50 #for $pedigree in $gatk_param_type.pedigree:
51 -p '--pedigree "${pedigree.pedigree_file}"'
52 #end for
53 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
54 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
55 #end for
56 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
57 #for $read_filter in $gatk_param_type.read_filter:
58 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
59 ###raise Exception( str( dir( $read_filter ) ) )
60 #for $name, $param in $read_filter.read_filter_type.iteritems():
61 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
62 #if hasattr( $param.input, 'truevalue' ):
63 ${param}
64 #else:
65 --${name} "${param}"
66 #end if
67 #end if
68 #end for
69 '
70 #end for
71 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
72 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
73 #end for
74
75 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
76 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
77 #end for
78
79 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
80
81 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
82 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
83 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
84 #end if
85 -p '
86 --baq "${gatk_param_type.baq}"
87 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
88 ${gatk_param_type.use_original_qualities}
89 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
90 --validation_strictness "${gatk_param_type.validation_strictness}"
91 --interval_merging "${gatk_param_type.interval_merging}"
92 ${gatk_param_type.disable_experimental_low_memory_sharding}
93 ${gatk_param_type.non_deterministic_random_seed}
94 '
95 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
96 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
97 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
98 #else
99 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
100 #end if
101 #end for
102 #end if
103
104 #if str( $reference_source.reference_source_selector ) == "history":
105 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
106 #end if
107 ##end standard gatk options
108
109 ##start analysis specific options
110 #if $analysis_param_type.analysis_param_type_selector == "advanced":
111 -p '
112 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
113 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
114 #end if
115 #if str( $analysis_param_type.default_platform ) != "default":
116 --default_platform "${analysis_param_type.default_platform}"
117 #end if
118 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
119 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
120 #end if
121 #if str( $analysis_param_type.force_platform ) != "default":
122 --force_platform "${analysis_param_type.force_platform}"
123 #end if
124 ${analysis_param_type.exception_if_no_tile}
125 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
126 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
127 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
128 #end if
129 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
130 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
131 #end if
132 #end if
133 --window_size_nqs "${analysis_param_type.window_size_nqs}"
134 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
135 '
136 #end if
137 #if not $snp_dataset_provided:
138 -p '--run_without_dbsnp_potentially_ruining_quality'
139 #end if
140 </command>
141 <inputs>
142 <conditional name="reference_source">
143 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
144 <option value="cached">Locally cached</option>
145 <option value="history">History</option>
146 </param>
147 <when value="cached">
148 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
149 <validator type="unspecified_build" />
150 <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 -->
151 </param>
152 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
153 <options from_data_table="gatk2_picard_indexes">
154 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
155 </options>
156 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
157 </param>
158 </when>
159 <when value="history">
160 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
161 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
162 <options>
163 <filter type="data_meta" key="dbkey" ref="input_bam" />
164 </options>
165 </param>
166 </when>
167 </conditional>
168 <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" />
169 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
170 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
171 <option value="ReadGroupCovariate" />
172 <option value="QualityScoreCovariate" />
173 <option value="CycleCovariate" />
174 <option value="DinucCovariate" />
175 <!-- covariates below were pulled from list option -->
176 <option value="HomopolymerCovariate" />
177 <option value="GCContentCovariate" />
178 <option value="MappingQualityCovariate" />
179 <option value="MinimumNQSCovariate" />
180 <option value="PositionCovariate" />
181 <option value="PrimerRoundCovariate" />
182 <option value="TileCovariate" />
183 </param>
184
185 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-knownSites,--knownSites &amp;lt;knownSites&amp;gt;">
186 <conditional name="rod_bind_type">
187 <param name="rod_bind_type_selector" type="select" label="Binding Type">
188 <option value="dbsnp" selected="True">dbSNP</option>
189 <option value="snps">SNPs</option>
190 <option value="indels">INDELs</option>
191 <option value="mask">Mask</option>
192 <option value="custom">Custom</option>
193 </param>
194 <when value="dbsnp">
195 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
196 </when>
197 <when value="snps">
198 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
199 </when>
200 <when value="indels">
201 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
202 </when>
203 <when value="mask">
204 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
205 </when>
206 <when value="custom">
207 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
208 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
209 </when>
210 </conditional>
211 </repeat>
212
213 <conditional name="gatk_param_type">
214 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
215 <option value="basic" selected="True">Basic</option>
216 <option value="advanced">Advanced</option>
217 </param>
218 <when value="basic">
219 <!-- Do nothing here -->
220 </when>
221 <when value="advanced">
222 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
223 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
224 </repeat>
225 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
226 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
227 </repeat>
228 <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;">
229 <option value="STRICT" selected="True">STRICT</option>
230 <option value="SILENT">SILENT</option>
231 </param>
232 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
233 <conditional name="read_filter_type">
234 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
235 <option value="BadCigar">BadCigar</option>
236 <option value="BadMate">BadMate</option>
237 <option value="DuplicateRead">DuplicateRead</option>
238 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
239 <option value="MalformedRead">MalformedRead</option>
240 <option value="MappingQuality">MappingQuality</option>
241 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
242 <option value="MappingQualityZero">MappingQualityZero</option>
243 <option value="MateSameStrand">MateSameStrand</option>
244 <option value="MaxInsertSize">MaxInsertSize</option>
245 <option value="MaxReadLength" selected="True">MaxReadLength</option>
246 <option value="MissingReadGroup">MissingReadGroup</option>
247 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
248 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
249 <option value="Platform454">Platform454</option>
250 <option value="Platform">Platform</option>
251 <option value="PlatformUnit">PlatformUnit</option>
252 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
253 <option value="ReadName">ReadName</option>
254 <option value="ReadStrand">ReadStrand</option>
255 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
256 <option value="Sample">Sample</option>
257 <option value="SingleReadGroup">SingleReadGroup</option>
258 <option value="UnmappedRead">UnmappedRead</option>
259 </param>
260 <when value="BadCigar">
261 <!-- no extra options -->
262 </when>
263 <when value="BadMate">
264 <!-- no extra options -->
265 </when>
266 <when value="DuplicateRead">
267 <!-- no extra options -->
268 </when>
269 <when value="FailsVendorQualityCheck">
270 <!-- no extra options -->
271 </when>
272 <when value="MalformedRead">
273 <!-- no extra options -->
274 </when>
275 <when value="MappingQuality">
276 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
277 </when>
278 <when value="MappingQualityUnavailable">
279 <!-- no extra options -->
280 </when>
281 <when value="MappingQualityZero">
282 <!-- no extra options -->
283 </when>
284 <when value="MateSameStrand">
285 <!-- no extra options -->
286 </when>
287 <when value="MaxInsertSize">
288 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
289 </when>
290 <when value="MaxReadLength">
291 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
292 </when>
293 <when value="MissingReadGroup">
294 <!-- no extra options -->
295 </when>
296 <when value="NoOriginalQualityScores">
297 <!-- no extra options -->
298 </when>
299 <when value="NotPrimaryAlignment">
300 <!-- no extra options -->
301 </when>
302 <when value="Platform454">
303 <!-- no extra options -->
304 </when>
305 <when value="Platform">
306 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
307 </when>
308 <when value="PlatformUnit">
309 <!-- no extra options -->
310 </when>
311 <when value="ReadGroupBlackList">
312 <!-- no extra options -->
313 </when>
314 <when value="ReadName">
315 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
316 </when>
317 <when value="ReadStrand">
318 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
319 </when>
320 <when value="ReassignMappingQuality">
321 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
322 </when>
323 <when value="Sample">
324 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
325 </when>
326 <when value="SingleReadGroup">
327 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
328 </when>
329 <when value="UnmappedRead">
330 <!-- no extra options -->
331 </when>
332 </conditional>
333 </repeat>
334 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
335 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
336 </repeat>
337 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
338 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
339 </repeat>
340
341 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
342 <option value="UNION" selected="True">UNION</option>
343 <option value="INTERSECTION">INTERSECTION</option>
344 </param>
345
346 <conditional name="downsampling_type">
347 <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;">
348 <option value="NONE" selected="True">NONE</option>
349 <option value="ALL_READS">ALL_READS</option>
350 <option value="BY_SAMPLE">BY_SAMPLE</option>
351 </param>
352 <when value="NONE">
353 <!-- no more options here -->
354 </when>
355 <when value="ALL_READS">
356 <conditional name="downsample_to_type">
357 <param name="downsample_to_type_selector" type="select" label="Downsample method">
358 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
359 <option value="downsample_to_coverage">Downsample by Coverage</option>
360 </param>
361 <when value="downsample_to_fraction">
362 <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;"/>
363 </when>
364 <when value="downsample_to_coverage">
365 <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;"/>
366 </when>
367 </conditional>
368 </when>
369 <when value="BY_SAMPLE">
370 <conditional name="downsample_to_type">
371 <param name="downsample_to_type_selector" type="select" label="Downsample method">
372 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
373 <option value="downsample_to_coverage">Downsample by Coverage</option>
374 </param>
375 <when value="downsample_to_fraction">
376 <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;"/>
377 </when>
378 <when value="downsample_to_coverage">
379 <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;"/>
380 </when>
381 </conditional>
382 </when>
383 </conditional>
384 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
385 <option value="OFF" selected="True">OFF</option>
386 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
387 <option value="RECALCULATE">RECALCULATE</option>
388 </param>
389 <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;" />
390 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
391 <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;"/>
392 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
393 <option value="STRICT" selected="True">STRICT</option>
394 <option value="LENIENT">LENIENT</option>
395 <option value="SILENT">SILENT</option>
396 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
397 </param>
398 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
399 <option value="ALL" selected="True">ALL</option>
400 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
401 </param>
402
403 <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;">
404 <conditional name="read_group_black_list_type">
405 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
406 <option value="file" selected="True">Filters in file</option>
407 <option value="text">Specify filters as a string</option>
408 </param>
409 <when value="file">
410 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
411 </when>
412 <when value="text">
413 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
414 </when>
415 </conditional>
416 </repeat>
417
418 <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"/>
419 <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"/>
420
421 </when>
422 </conditional>
423
424 <conditional name="analysis_param_type">
425 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
426 <option value="basic" selected="True">Basic</option>
427 <option value="advanced">Advanced</option>
428 </param>
429 <when value="basic">
430 <!-- Do nothing here -->
431 </when>
432 <when value="advanced">
433 <conditional name="default_read_group_type">
434 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
435 <option value="default" selected="True">Don't Set</option>
436 <option value="set">Set</option>
437 </param>
438 <when value="default">
439 <!-- do nothing here -->
440 </when>
441 <when value="set">
442 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
443 </when>
444 </conditional>
445 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
446 <option value="default" selected="True">Don't Set</option>
447 <option value="illumina">illumina</option>
448 <option value="454">454</option>
449 <option value="solid">solid</option>
450 </param>
451 <conditional name="force_read_group_type">
452 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
453 <option value="default" selected="True">Don't Force</option>
454 <option value="set">Force</option>
455 </param>
456 <when value="default">
457 <!-- do nothing here -->
458 </when>
459 <when value="set">
460 <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
461 </when>
462 </conditional>
463 <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
464 <option value="default" selected="True">Don't Force</option>
465 <option value="illumina">illumina</option>
466 <option value="454">454</option>
467 <option value="solid">solid</option>
468 </param>
469 <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
470 <conditional name="solid_options_type">
471 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
472 <option value="default" selected="True">Don't Set</option>
473 <option value="set">Set</option>
474 </param>
475 <when value="default">
476 <!-- do nothing here -->
477 </when>
478 <when value="set">
479 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
480 <option value="default" selected="True">Don't set</option>
481 <option value="DO_NOTHING">DO_NOTHING</option>
482 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
483 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
484 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
485 </param>
486 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
487 <option value="default" selected="True">Don't set</option>
488 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
489 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
490 <option value="PURGE_READ">PURGE_READ</option>
491 </param>
492 </when>
493 </conditional>
494 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/>
495 <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
496 </when>
497 </conditional>
498 </inputs>
499 <outputs>
500 <data format="csv" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
501 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
502 </outputs>
503 <tests>
504 <test>
505 <param name="reference_source_selector" value="history" />
506 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
507 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
508 <param name="rod_bind_type_selector" value="dbsnp" />
509 <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
510 <param name="standard_covs" value="True" />
511 <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
512 <param name="gatk_param_type_selector" value="basic" />
513 <param name="analysis_param_type_selector" value="basic" />
514 <output name="output_recal" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" />
515 <output name="output_log" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains" compare="contains" />
516 </test>
517 </tests>
518 <help>
519 .. class:: warningmark
520
521 "This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."
522 However, if you do not provide this file, the '--run_without_dbsnp_potentially_ruining_quality' flag will be automatically used, and the command will be allowed to run.
523
524 **What it does**
525
526 This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide) Since there is a large amount of data one can then calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score) The first non-comment line of the output file gives the name of the covariates that were used for this calculation. Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified Note: This walker is designed to be used in conjunction with TableRecalibrationWalker.
527
528 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html&gt;`_.
529
530 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
531
532 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
533
534 ------
535
536 **Inputs**
537
538 GenomeAnalysisTK: BaseRecalibrator accepts an aligned BAM input file.
539
540
541 **Outputs**
542
543 The output is in CSV format.
544
545
546 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
547
548 -------
549
550 **Settings**::
551
552
553 default_read_group If a read has no read group then default to the provided String.
554 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
555 force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
556 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
557 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
558 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
559 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
560 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
561 solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
562 recal_file Filename for the input covariates table recalibration .csv file
563 out The output CSV file
564 standard_covs Use the standard set of covariates in addition to the ones listed using the -cov argument
565 run_without_dbsnp_potentially_ruining_quality If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.
566
567 ------
568
569 **Citation**
570
571 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;`_
572
573 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
574
575 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
576
577 </help>
578 </tool>