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comparison freebayes.xml @ 17:4c80a1387285 draft

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author devteam
date Fri, 20 Feb 2015 19:02:43 -0500
parents 6d9407020066
children 8fb829f953d6
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16:6d9407020066 17:4c80a1387285
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="freebayes" name="FreeBayes" version="0.3"> 2 <tool id="freebayes" name="FreeBayes" version="0.4">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.9.18_0059bdf">freebayes</requirement> 4 <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements> 6 </requirements>
7 <description> - bayesian genetic variant detector</description> 7 <description> - bayesian genetic variant detector</description>
8 <command> 8 <command>
9 ##set up input files 9 ##set up input files
74 --report-monomorphic 74 --report-monomorphic
75 --standard-filters 75 --standard-filters
76 --min-coverage "${options_type.min_coverage}" 76 --min-coverage "${options_type.min_coverage}"
77 77
78 ## Command line direct text entry is not allowed at this time for security reasons 78 ## Command line direct text entry is not allowed at this time for security reasons
79
80 ## #elif str( $options_type.options_type_selector ) == "cline":
81
82 ## ${options_type.cline}
83
84 ## @optional_inputs_outputs@
85 79
86 #elif str( $options_type.options_type_selector ) == "full": 80 #elif str( $options_type.options_type_selector ) == "full":
87
88 ##optional inputs and outputs
89 81
90 @optional_inputs_outputs@ 82 #if $options_type.optional_inputs.optional_inputs_selector:
91
92 ## REPORTING
93
94 #if str( $options_type.reporting.reporting_selector ) == "True":
95 --pvar ${options_type.reporting.pvar}
96 #end if
97
98 ## POPULATION MODEL
99
100 #if str( $options_type.population_model.population_model_selector ) == "True":
101 --theta "${options_type.population_model.T}"
102 --ploidy "${options_type.population_model.P}"
103 ${options_type.population_model.J}
104 ${options_type.population_model.K}
105
106 #end if
107
108 ## REFERENCE ALLELE
109
110 #if str( $options_type.reference_allele.reference_allele_selector ) == "True":
111 ${options_type.reference_allele.Z}
112 --reference-quality "${options_type.reference_allele.reference_quality}"
113 #end if
114
115 ## ALLELE SCOPE
116
117 #if str( $options_type.allele_scope.allele_scope_selector ) == "True":
118 ${options_type.allele_scope.I}
119 ${options_type.allele_scope.i}
120 ${options_type.allele_scope.X}
121 ${options_type.allele_scope.u}
122 -n "${options_type.allele_scope.n}"
123 --haplotype-length "${options_type.allele_scope.haplotype_length}"
124 --min-repeat-size "${options_type.allele_scope.min_repeat_length}"
125 --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
126 ${options_type.allele_scope.no_partial_observations}
127 #end if
128
129 ## REALIGNMENT
130
131 ${options_type.O}
132
133 ##INPUT FILTERS
134
135 #if str( $options_type.input_filters.input_filters_selector ) == "True":
136 ${options_type.input_filters.use_duplicate_reads}
137 -m "${options_type.input_filters.m}"
138 -q "${options_type.input_filters.q}"
139 -R "${options_type.input_filters.R}"
140 -Y "${options_type.input_filters.Y}"
141
142 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "True":
143 -Q "${options_type.input_filters.mismatch_filters.Q}"
144 -U "${options_type.input_filters.mismatch_filters.U}"
145 -z "${options_type.input_filters.mismatch_filters.z}"
146 --read-snp-limit "${options_type.input_filters.mismatch_filters.read_snp_limit}"
147 #end if
148
149 -e "${options_type.input_filters.e}"
150 -F "${options_type.input_filters.F}"
151 -C "${options_type.input_filters.C}"
152 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
153 -G "${options_type.input_filters.G}"
154 --min-coverage "${options_type.input_filters.min_coverage}"
155 #end if
156
157 ## POPULATION AND MAPPABILITY PRIORS
158
159 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "True":
160 ${options_type.population_mappability_priors.k}
161 ${options_type.population_mappability_priors.w}
162 ${options_type.population_mappability_priors.V}
163 ${options_type.population_mappability_priors.a}
164 #end if
165
166 ## GENOTYPE LIKELIHOODS
167
168 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
169 --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
170 ${$options_type.genotype_likelihoods.experimental_gls}
171 --prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}"
172 #end if
173
174 ## ALGORITHMIC FEATURES
175
176 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
177 ${options_type.algorithmic_features.report_genotype_likelihood_max}
178 -B "${options_type.algorithmic_features.B}"
179 --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
180 -W "${options_type.algorithmic_features.W}"
181 ${options_type.algorithmic_features.N}
182
183 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "True":
184 -S "${options_type.algorithmic_features.genotype_variant_threshold.S}"
185 #end if
186
187 ${options_type.algorithmic_features.j}
188 ${options_type.algorithmic_features.H}
189 -D "${options_type.algorithmic_features.D}"
190 ${options_type.algorithmic_features.genotype_qualities}
191 #end if
192 #end if
193
194 </command>
195
196 <macros>
197 <token name="@optional_inputs_outputs@">
198 ## This token gets injected in commane in two instances: when options_type.options_type_selector == "full" and "cline" ( cline is not supported at this time )
199
200 #if $options_type.optional_inputs.optional_inputs_selector:
201 83
202 #if $options_type.optional_inputs.output_trace_option: 84 #if $options_type.optional_inputs.output_trace_option:
203 --trace "${output_trace}" 85 --trace "${output_trace}"
204 #end if 86 #end if
205 87
235 #if $options_type.optional_inputs.contamination_estimates: 117 #if $options_type.optional_inputs.contamination_estimates:
236 --contamination-estimates "${options_type.optional_inputs.contamination_estimates}" 118 --contamination-estimates "${options_type.optional_inputs.contamination_estimates}"
237 #end if 119 #end if
238 120
239 #end if 121 #end if
240 </token> 122
241 <xml name="optional_file_inputs"> 123 ## REPORTING
242 <conditional name="optional_inputs"> 124
125 #if str( $options_type.reporting.reporting_selector ) == "True":
126 --pvar ${options_type.reporting.pvar}
127 #end if
128
129 ## POPULATION MODEL
130
131 #if str( $options_type.population_model.population_model_selector ) == "True":
132 --theta "${options_type.population_model.T}"
133 --ploidy "${options_type.population_model.P}"
134 ${options_type.population_model.J}
135 ${options_type.population_model.K}
136
137 #end if
138
139 ## REFERENCE ALLELE
140
141 #if str( $options_type.reference_allele.reference_allele_selector ) == "True":
142 ${options_type.reference_allele.Z}
143 --reference-quality "${options_type.reference_allele.reference_quality}"
144 #end if
145
146 ## ALLELE SCOPE
147
148 #if str( $options_type.allele_scope.allele_scope_selector ) == "True":
149 ${options_type.allele_scope.I}
150 ${options_type.allele_scope.i}
151 ${options_type.allele_scope.X}
152 ${options_type.allele_scope.u}
153 -n "${options_type.allele_scope.n}"
154 --haplotype-length "${options_type.allele_scope.haplotype_length}"
155 --min-repeat-size "${options_type.allele_scope.min_repeat_length}"
156 --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
157 ${options_type.allele_scope.no_partial_observations}
158 #end if
159
160 ## REALIGNMENT
161
162 ${options_type.O}
163
164 ##INPUT FILTERS
165
166 #if str( $options_type.input_filters.input_filters_selector ) == "True":
167 ${options_type.input_filters.use_duplicate_reads}
168 -m "${options_type.input_filters.m}"
169 -q "${options_type.input_filters.q}"
170 -R "${options_type.input_filters.R}"
171 -Y "${options_type.input_filters.Y}"
172
173 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "True":
174 -Q "${options_type.input_filters.mismatch_filters.Q}"
175 -U "${options_type.input_filters.mismatch_filters.U}"
176 -z "${options_type.input_filters.mismatch_filters.z}"
177 --read-snp-limit "${options_type.input_filters.mismatch_filters.read_snp_limit}"
178 #end if
179
180 -e "${options_type.input_filters.e}"
181 -F "${options_type.input_filters.F}"
182 -C "${options_type.input_filters.C}"
183 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
184 -G "${options_type.input_filters.G}"
185 --min-coverage "${options_type.input_filters.min_coverage}"
186 #end if
187
188 ## POPULATION AND MAPPABILITY PRIORS
189
190 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "True":
191 ${options_type.population_mappability_priors.k}
192 ${options_type.population_mappability_priors.w}
193 ${options_type.population_mappability_priors.V}
194 ${options_type.population_mappability_priors.a}
195 #end if
196
197 ## GENOTYPE LIKELIHOODS
198
199 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
200 --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
201 ${$options_type.genotype_likelihoods.experimental_gls}
202 --prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}"
203 #end if
204
205 ## ALGORITHMIC FEATURES
206
207 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
208 ${options_type.algorithmic_features.report_genotype_likelihood_max}
209 -B "${options_type.algorithmic_features.B}"
210 --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
211 -W "${options_type.algorithmic_features.W}"
212 ${options_type.algorithmic_features.N}
213
214 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "True":
215 -S "${options_type.algorithmic_features.genotype_variant_threshold.S}"
216 #end if
217
218 ${options_type.algorithmic_features.j}
219 ${options_type.algorithmic_features.H}
220 -D "${options_type.algorithmic_features.D}"
221 ${options_type.algorithmic_features.genotype_qualities}
222 #end if
223 #end if
224
225 </command>
226
227 <inputs>
228 <conditional name="reference_source">
229 <param name="reference_source_selector" type="select" label="Load reference genome from">
230 <option value="cached">Local cache</option>
231 <option value="history">History</option>
232 </param>
233 <when value="cached">
234 <repeat name="input_bams" title="Sample BAM file" min="1">
235 <param name="input_bam" type="data" format="bam" label="BAM file">
236 <validator type="unspecified_build" />
237 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
238 </param>
239 </repeat>
240
241 <param name="ref_file" type="select" label="Using reference genome">
242 <options from_data_table="fasta_indexes"></options>
243 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
244 </param>
245 </when>
246 <when value="history"> <!-- FIX ME!!!! -->
247 <repeat name="input_bams" title="Sample BAM file" min="1">
248 <param name="input_bam" type="data" format="bam" label="BAM file" />
249 </repeat>
250 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
251 </when>
252 </conditional>
253
254 <conditional name="target_limit_type">
255 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
256 <option value="do_not_limit" selected="True">Do not limit</option>
257 <option value="limit_by_target_file">Limit by target file</option>
258 <option value="limit_by_region">Limit to region</option>
259 </param>
260 <when value="do_not_limit">
261 <!-- Do nothing here -->
262 </when>
263 <when value="limit_by_target_file">
264 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/>
265 </when>
266 <when value="limit_by_region">
267 <param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? -->
268 <param name="region_start" type="integer" label="Region Start" value="" />
269 <param name="region_end" type="integer" label="Region End" value="" />
270 </when>
271 </conditional>
272
273 <conditional name="options_type">
274 <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need" >
275 <option value="simple" selected="True">1:Simple diploid calling</option>
276 <option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option>
277 <option value="naive">3:Frequency-based pooled calling</option>
278 <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
279 <option value="full">5:Complete list of all options</option>
280 <!-- We will not alloow command line text boxes at this time
281 <option value="cline">6:Input parameters on the command line</option>
282 -->
283 </param>
284 <when value="full">
285
286 <conditional name="optional_inputs">
243 <param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide additional inputs?" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates" /> 287 <param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide additional inputs?" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates" />
244 <when value="set"> 288 <when value="set">
245 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" help="--failed-alleles" /> 289 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" help="--failed-alleles" />
246 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--trace"/> 290 <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--trace"/>
247 <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/> 291 <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/>
268 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." /> 312 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." />
269 </when> 313 </when>
270 <when value="do_not_set"> 314 <when value="do_not_set">
271 <!-- do nothing --> 315 <!-- do nothing -->
272 </when> 316 </when>
273 </conditional> 317 </conditional>
274 </xml>
275 </macros>
276
277 <inputs>
278 <conditional name="reference_source">
279 <param name="reference_source_selector" type="select" label="Load reference genome from">
280 <option value="cached">Local cache</option>
281 <option value="history">History</option>
282 </param>
283 <when value="cached">
284 <repeat name="input_bams" title="Sample BAM file" min="1">
285 <param name="input_bam" type="data" format="bam" label="BAM file">
286 <validator type="unspecified_build" />
287 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
288 </param>
289 </repeat>
290
291 <param name="ref_file" type="select" label="Using reference genome">
292 <options from_data_table="fasta_indexes"></options>
293 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
294 </param>
295 </when>
296 <when value="history"> <!-- FIX ME!!!! -->
297 <repeat name="input_bams" title="Sample BAM file" min="1">
298 <param name="input_bam" type="data" format="bam" label="BAM file" />
299 </repeat>
300 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
301 </when>
302 </conditional>
303
304 <conditional name="target_limit_type">
305 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
306 <option value="do_not_limit" selected="True">Do not limit</option>
307 <option value="limit_by_target_file">Limit by target file</option>
308 <option value="limit_by_region">Limit to region</option>
309 </param>
310 <when value="do_not_limit">
311 <!-- Do nothing here -->
312 </when>
313 <when value="limit_by_target_file">
314 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/>
315 </when>
316 <when value="limit_by_region">
317 <param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? -->
318 <param name="region_start" type="integer" label="Region Start" value="" />
319 <param name="region_end" type="integer" label="Region End" value="" />
320 </when>
321 </conditional>
322
323 <conditional name="options_type">
324 <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need" >
325 <option value="simple" selected="True">1:Simple diploid calling</option>
326 <option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option>
327 <option value="naive">3:Frequency-based pooled calling</option>
328 <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
329 <option value="full">5:Complete list of all options</option>
330 <!-- We will not alloow command line text boxes at this time
331 <option value="cline">6:Input parameters on the command line</option>
332 -->
333 </param>
334 <when value="full">
335
336 <expand macro="optional_file_inputs" /> <!-- see macros section -->
337 318
338 <!-- reporting --> 319 <!-- reporting -->
339 320
340 <conditional name="reporting"> 321 <conditional name="reporting">
341 <param name="reporting_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set reporting option?" help="Sets -P --pvar option" /> 322 <param name="reporting_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set reporting option?" help="Sets -P --pvar option" />
504 </when> 485 </when>
505 <when value="naive_w_filters"> 486 <when value="naive_w_filters">
506 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters--> 487 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
507 <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " /> 488 <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " />
508 </when> 489 </when>
490 </conditional>
491
492 </inputs>
509 493
510 <!-- We will not allow command line textboxes at this time
511 <when value="cline">
512
513 <expand macro="optional_file_inputs" />
514
515 <param name="cline" size="60" type="text" value="-m 20 -q 30" label="Type command line tags here" help="All paremeters that DO NOT involve filenames can be typed here. Use &quot;Do you want to provide additional inputs?&quot; section above to control input and output files. For full syntax check help section below">
516 <sanitizer>
517 <valid initial="string.printable">
518 <remove value="&apos;"/>
519 </valid>
520 <mapping initial="none">
521 <add source="&apos;" target="__sq__"/>
522 </mapping>
523 </sanitizer>
524 </param>
525 </when>
526 -->
527
528 </conditional>
529
530 </inputs>
531 <outputs> 494 <outputs>
532 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> 495 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
533 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> 496 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
534 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] is True and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter> 497 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] is True and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
535 </data> 498 </data>
543 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> 506 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
544 <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/> 507 <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
545 <param name="options_type_selector" value="simple"/> 508 <param name="options_type_selector" value="simple"/>
546 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/> 509 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
547 </test> 510 </test>
511 <test>
512 <param name="reference_source_selector" value="history" />
513 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
514 <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
515 <param name="options_type_selector" value="naive_w_filters"/>
516 <param name="min_coverage" value="14"/>
517 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
518 </test>
548 </tests> 519 </tests>
549 <stdio> 520 <stdio>
550 <exit_code range="1:" /> 521 <exit_code range="1:" />
551 </stdio> 522 </stdio>
552 <help> 523 <help>
554 525
555 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 526 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
556 527
557 See https://github.com/ekg/freebayes for details on FreeBayes. 528 See https://github.com/ekg/freebayes for details on FreeBayes.
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559 This Galaxy instance of FreeBayes corresponds to release 0.9.18 530 This Galaxy instance of FreeBayes corresponds to release 0.9.20
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563 **Description** 534 **Description**
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