Mercurial > repos > iuc > gatk2
comparison unified_genotyper.xml @ 0:340633249b3d draft
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author | bgruening |
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date | Mon, 02 Dec 2013 06:18:36 -0500 |
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children | 8bcc13094767 |
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1 <tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.7"> | |
2 <description>SNP and indel caller</description> | |
3 <expand macro="requirements" /> | |
4 <macros> | |
5 <import>gatk2_macros.xml</import> | |
6 </macros> | |
7 <command interpreter="python"> | |
8 gatk2_wrapper.py | |
9 --stdout "${output_log}" | |
10 #for $i, $input_bam in enumerate( $reference_source.input_bams ): | |
11 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" | |
12 #if str( $input_bam.input_bam.metadata.bam_index ) != "None": | |
13 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index | |
14 #end if | |
15 #end for | |
16 -p ' | |
17 @JAR_PATH@ | |
18 -T "UnifiedGenotyper" | |
19 @THREADS@ | |
20 --out "${output_vcf}" | |
21 --metrics_file "${output_metrics}" | |
22 \$GATK2_SITE_OPTIONS | |
23 | |
24 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 | |
25 --num_cpu_threads_per_data_thread 6 | |
26 | |
27 #if $reference_source.reference_source_selector != "history": | |
28 -R "${reference_source.ref_file.fields.path}" | |
29 #end if | |
30 --genotype_likelihoods_model "${genotype_likelihoods_model}" | |
31 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" | |
32 --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" | |
33 ' | |
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 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 | |
42 -d "--dbsnp:${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[$rod_bind_name]}" | |
43 #end for | |
44 | |
45 #include source=$standard_gatk_options# | |
46 ##start analysis specific options | |
47 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
48 -p ' | |
49 --p_nonref_model "${analysis_param_type.p_nonref_model}" | |
50 --heterozygosity "${analysis_param_type.heterozygosity}" | |
51 --pcr_error_rate "${analysis_param_type.pcr_error_rate}" | |
52 --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}" | |
53 #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES': | |
54 --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}" | |
55 #end if | |
56 --output_mode "${analysis_param_type.output_mode}" | |
57 ${analysis_param_type.compute_SLOD} | |
58 --min_base_quality_score "${analysis_param_type.min_base_quality_score}" | |
59 --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}" | |
60 --max_alternate_alleles "${analysis_param_type.max_alternate_alleles}" | |
61 --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}" | |
62 --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}" | |
63 --indelGapContinuationPenalty "${analysis_param_type.indelGapContinuationPenalty}" | |
64 --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}" | |
65 --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" | |
66 ${analysis_param_type.doContextDependentGapPenalties} | |
67 #if str( $analysis_param_type.annotation ) != "None": | |
68 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): | |
69 --annotation "${annotation}" | |
70 #end for | |
71 #end if | |
72 #for $additional_annotation in $analysis_param_type.additional_annotations: | |
73 --annotation "${additional_annotation.additional_annotation_name}" | |
74 #end for | |
75 #if str( $analysis_param_type.group ) != "None": | |
76 #for $group in str( $analysis_param_type.group ).split( ','): | |
77 --group "${group}" | |
78 #end for | |
79 #end if | |
80 #if str( $analysis_param_type.exclude_annotations ) != "None": | |
81 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): | |
82 --excludeAnnotation "${annotation}" | |
83 #end for | |
84 #end if | |
85 ${analysis_param_type.multiallelic} | |
86 #if str( $analysis_param_type.sample_ploidy ) != '': | |
87 --sample_ploidy "$analysis_param_type.sample_ploidy" | |
88 #end if | |
89 ' | |
90 ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': | |
91 ## -p '--annotation "SnpEff"' | |
92 ## -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}" | |
93 ## #else: | |
94 ## -p '--excludeAnnotation "SnpEff"' | |
95 ## #end if | |
96 #end if | |
97 </command> | |
98 <inputs> | |
99 <conditional name="reference_source"> | |
100 <expand macro="reference_source_selector_param" /> | |
101 <when value="cached"> | |
102 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> | |
103 <param name="input_bam" type="data" format="bam" label="BAM file"> | |
104 <validator type="unspecified_build" /> | |
105 <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 --> | |
106 </param> | |
107 </repeat> | |
108 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
109 <options from_data_table="gatk2_picard_indexes"> | |
110 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> | |
111 </options> | |
112 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
113 </param> | |
114 </when> | |
115 <when value="history"> <!-- FIX ME!!!! --> | |
116 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> | |
117 <param name="input_bam" type="data" format="bam" label="BAM file" > | |
118 </param> | |
119 </repeat> | |
120 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
121 </when> | |
122 </conditional> | |
123 | |
124 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-D,--dbsnp &lt;dbsnp&gt;"> | |
125 <conditional name="rod_bind_type"> | |
126 <param name="rod_bind_type_selector" type="select" label="Binding Type"> | |
127 <option value="dbsnp" selected="True">dbSNP</option> | |
128 <option value="snps">SNPs</option> | |
129 <option value="indels">INDELs</option> | |
130 <option value="custom">Custom</option> | |
131 </param> | |
132 <when value="dbsnp"> | |
133 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
134 </when> | |
135 <when value="snps"> | |
136 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
137 </when> | |
138 <when value="indels"> | |
139 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
140 </when> | |
141 <when value="custom"> | |
142 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> | |
143 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
144 </when> | |
145 </conditional> | |
146 </repeat> | |
147 | |
148 <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &lt;genotype_likelihoods_model&gt;"> | |
149 <option value="BOTH" selected="True">BOTH</option> | |
150 <option value="SNP">SNP</option> | |
151 <option value="INDEL">INDEL</option> | |
152 </param> | |
153 | |
154 <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &lt;standard_min_confidence_threshold_for_calling&gt;" /> | |
155 <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &lt;standard_min_confidence_threshold_for_emitting&gt;" /> | |
156 | |
157 | |
158 <expand macro="gatk_param_type_conditional" /> | |
159 | |
160 <expand macro="analysis_type_conditional"> | |
161 <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &lt;p_nonref_model&gt;"> | |
162 <option value="EXACT_GENERAL_PLOIDY" selected="True">EXACT_GENERAL_PLOIDY (supports any sample ploidy)</option> | |
163 <option value="EXACT_REFERENCE">EXACT_REFERENCE (multi-allelic EXACT model. Extremely slow for many alternate alleles)</option> | |
164 </param> | |
165 <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &lt;heterozygosity&gt;" /> | |
166 <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &lt;pcr_error_rate&gt;" /> | |
167 <conditional name="genotyping_mode_type"> | |
168 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &lt;genotyping_mode&gt;"> | |
169 <option value="DISCOVERY" selected="True">DISCOVERY</option> | |
170 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> | |
171 </param> | |
172 <when value="DISCOVERY"> | |
173 <!-- Do nothing here --> | |
174 </when> | |
175 <when value="GENOTYPE_GIVEN_ALLELES"> | |
176 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" /> | |
177 </when> | |
178 </conditional> | |
179 <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode &lt;output_mode&gt;"> | |
180 <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option> | |
181 <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option> | |
182 <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option> | |
183 </param> | |
184 <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" /> | |
185 <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &lt;min_base_quality_score&gt;" /> | |
186 <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction &lt;max_deletion_fraction&gt;)" /> | |
187 <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" /> | |
188 <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &lt;min_indel_count_for_genotyping&gt;" /> | |
189 <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &lt;indel_heterozygosity&gt;)"/> | |
190 <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty"> | |
191 <help>Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help> | |
192 <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> | |
193 </param> | |
194 <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="--indelGapOpenPenalty" > | |
195 <help>Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help> | |
196 <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> | |
197 </param> | |
198 <!-- indelHaplotypeSize - Gone in GATK 2.4? --> | |
199 <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> | |
200 <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> | |
201 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> | |
202 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | |
203 <options from_data_table="gatk2_annotations"> | |
204 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | |
205 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> | |
206 </options> | |
207 </param> | |
208 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> | |
209 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> | |
210 </repeat> | |
211 <!-- | |
212 <conditional name="snpEff_rod_bind_type"> | |
213 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> | |
214 <option value="set_snpEff">Set snpEff</option> | |
215 <option value="exclude_snpEff" selected="True">Don't set snpEff</option> | |
216 </param> | |
217 <when value="exclude_snpEff"> | |
218 </when> | |
219 <when value="set_snpEff"> | |
220 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> | |
221 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> | |
222 </when> | |
223 </conditional> | |
224 --> | |
225 <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;"> | |
226 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> | |
227 <option value="Standard">Standard</option> | |
228 <option value="Experimental">Experimental</option> | |
229 <option value="WorkInProgress">WorkInProgress</option> | |
230 <option value="RankSumTest">RankSumTest</option> | |
231 <!-- <option value="none">none</option> --> | |
232 </param> | |
233 <!-- <param name="family_string" type="text" value="" label="Family String"/> --> | |
234 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > | |
235 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | |
236 <options from_data_table="gatk2_annotations"> | |
237 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | |
238 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> | |
239 </options> | |
240 </param> | |
241 <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" /> | |
242 </expand> | |
243 </inputs> | |
244 <outputs> | |
245 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> | |
246 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /> | |
247 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
248 </outputs> | |
249 <trackster_conf/> | |
250 <tests> | |
251 <test> | |
252 <param name="reference_source_selector" value="history" /> | |
253 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
254 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> | |
255 <param name="rod_bind_type_selector" value="dbsnp" /> | |
256 <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> | |
257 <param name="standard_min_confidence_threshold_for_calling" value="0" /> | |
258 <param name="standard_min_confidence_threshold_for_emitting" value="4" /> | |
259 <param name="gatk_param_type_selector" value="basic" /> | |
260 <param name="analysis_param_type_selector" value="advanced" /> | |
261 <param name="genotype_likelihoods_model" value="BOTH" /> | |
262 <param name="p_nonref_model" value="EXACT" /> | |
263 <param name="heterozygosity" value="0.001" /> | |
264 <param name="pcr_error_rate" value="0.0001" /> | |
265 <param name="genotyping_mode" value="DISCOVERY" /> | |
266 <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" /> | |
267 <param name="compute_SLOD" /> | |
268 <param name="min_base_quality_score" value="17" /> | |
269 <param name="max_deletion_fraction" value="-1" /> | |
270 <param name="min_indel_count_for_genotyping" value="2" /> | |
271 <param name="indel_heterozygosity" value="0.000125" /> | |
272 <param name="indelGapContinuationPenalty" value="10" /> | |
273 <param name="indelGapOpenPenalty" value="3" /> | |
274 <param name="indelHaplotypeSize" value="80" /> | |
275 <param name="doContextDependentGapPenalties" /> | |
276 <!-- <param name="annotation" value="" /> | |
277 <param name="group" value="" /> --> | |
278 <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> | |
279 <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> | |
280 <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" /> | |
281 </test> | |
282 </tests> | |
283 <help> | |
284 **What it does** | |
285 | |
286 A variant caller which unifies the approaches of several disparate callers. Works for single-sample and multi-sample data. The user can choose from several different incorporated calculation models. | |
287 | |
288 For more information on the GATK Unified Genotyper, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html>`_. | |
289 | |
290 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
291 | |
292 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
293 | |
294 ------ | |
295 | |
296 **Inputs** | |
297 | |
298 GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file. | |
299 | |
300 | |
301 **Outputs** | |
302 | |
303 The output is in VCF format. | |
304 | |
305 | |
306 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
307 | |
308 ------- | |
309 | |
310 **Settings**:: | |
311 | |
312 genotype_likelihoods_model Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH) | |
313 p_nonref_model Non-reference probability calculation model to employ -- EXACT_GENERAL_PLOIDY is the default option, while EXACT_REFERENCE is also available. (EXACT_INDEPENDENT,EXACT_REFERENCE,EXACT_ORIGINAL,EXACT_GENERAL_PLOIDY) | |
314 heterozygosity Heterozygosity value used to compute prior likelihoods for any locus | |
315 pcr_error_rate The PCR error rate to be used for computing fragment-based likelihoods | |
316 genotyping_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES) | |
317 output_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (EMIT_VARIANTS_ONLY|EMIT_ALL_CONFIDENT_SITES|EMIT_ALL_SITES) | |
318 standard_min_confidence_threshold_for_calling The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called | |
319 standard_min_confidence_threshold_for_emitting The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold) | |
320 noSLOD If provided, we will not calculate the SLOD | |
321 min_base_quality_score Minimum base quality required to consider a base for calling | |
322 max_deletion_fraction Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05] | |
323 min_indel_count_for_genotyping Minimum number of consensus indels required to trigger genotyping run | |
324 indel_heterozygosity Heterozygosity for indel calling | |
325 indelGapContinuationPenalty Indel gap continuation penalty | |
326 indelGapOpenPenalty Indel gap open penalty | |
327 indelHaplotypeSize Indel haplotype size | |
328 doContextDependentGapPenalties Vary gap penalties by context | |
329 indel_recal_file Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE | |
330 indelDebug Output indel debug info | |
331 out File to which variants should be written | |
332 annotation One or more specific annotations to apply to variant calls | |
333 group One or more classes/groups of annotations to apply to variant calls | |
334 | |
335 @CITATION_SECTION@ | |
336 </help> | |
337 </tool> |