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comparison freebayes.xml @ 3:9f3d6c3098ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:37:39 -0500
parents 14f952d2a9db
children c171daf263dd
comparison
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2:14f952d2a9db 3:9f3d6c3098ac
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="0.4.1">
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 83
92 ## REPORTING 84 ${options_type.optional_inputs.report_monomorphic}
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 85
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
202 #if $options_type.optional_inputs.output_trace_option: 86 #if $options_type.optional_inputs.output_trace_option:
203 --trace "${output_trace}" 87 --trace "${output_trace}"
204 #end if 88 #end if
205 89
206 #if $options_type.optional_inputs.output_failed_alleles_option: 90 #if $options_type.optional_inputs.output_failed_alleles_option:
235 #if $options_type.optional_inputs.contamination_estimates: 119 #if $options_type.optional_inputs.contamination_estimates:
236 --contamination-estimates "${options_type.optional_inputs.contamination_estimates}" 120 --contamination-estimates "${options_type.optional_inputs.contamination_estimates}"
237 #end if 121 #end if
238 122
239 #end if 123 #end if
240 </token> 124
241 <xml name="optional_file_inputs"> 125 ## REPORTING
242 <conditional name="optional_inputs"> 126
127
128 #if str( $options_type.reporting.reporting_selector ) == "True":
129 --pvar ${options_type.reporting.pvar}
130 #end if
131
132 ## POPULATION MODEL
133
134 #if str( $options_type.population_model.population_model_selector ) == "True":
135 --theta "${options_type.population_model.T}"
136 --ploidy "${options_type.population_model.P}"
137 ${options_type.population_model.J}
138 ${options_type.population_model.K}
139
140 #end if
141
142 ## REFERENCE ALLELE
143
144 #if str( $options_type.reference_allele.reference_allele_selector ) == "True":
145 ${options_type.reference_allele.Z}
146 --reference-quality "${options_type.reference_allele.reference_quality}"
147 #end if
148
149 ## ALLELE SCOPE
150
151 #if str( $options_type.allele_scope.allele_scope_selector ) == "True":
152 ${options_type.allele_scope.I}
153 ${options_type.allele_scope.i}
154 ${options_type.allele_scope.X}
155 ${options_type.allele_scope.u}
156 -n "${options_type.allele_scope.n}"
157 --haplotype-length "${options_type.allele_scope.haplotype_length}"
158 --min-repeat-size "${options_type.allele_scope.min_repeat_length}"
159 --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
160 ${options_type.allele_scope.no_partial_observations}
161 #end if
162
163 ## REALIGNMENT
164
165 ${options_type.O}
166
167 ##INPUT FILTERS
168
169 #if str( $options_type.input_filters.input_filters_selector ) == "True":
170 ${options_type.input_filters.use_duplicate_reads}
171 -m "${options_type.input_filters.m}"
172 -q "${options_type.input_filters.q}"
173 -R "${options_type.input_filters.R}"
174 -Y "${options_type.input_filters.Y}"
175
176 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "True":
177 -Q "${options_type.input_filters.mismatch_filters.Q}"
178 -U "${options_type.input_filters.mismatch_filters.U}"
179 -z "${options_type.input_filters.mismatch_filters.z}"
180 --read-snp-limit "${options_type.input_filters.mismatch_filters.read_snp_limit}"
181 #end if
182
183 -e "${options_type.input_filters.e}"
184 -F "${options_type.input_filters.F}"
185 -C "${options_type.input_filters.C}"
186 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
187 -G "${options_type.input_filters.G}"
188 --min-coverage "${options_type.input_filters.min_coverage}"
189 #end if
190
191 ## POPULATION AND MAPPABILITY PRIORS
192
193 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "True":
194 ${options_type.population_mappability_priors.k}
195 ${options_type.population_mappability_priors.w}
196 ${options_type.population_mappability_priors.V}
197 ${options_type.population_mappability_priors.a}
198 #end if
199
200 ## GENOTYPE LIKELIHOODS
201
202 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
203 --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
204 ${$options_type.genotype_likelihoods.experimental_gls}
205 --prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}"
206 #end if
207
208 ## ALGORITHMIC FEATURES
209
210 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
211 ${options_type.algorithmic_features.report_genotype_likelihood_max}
212 -B "${options_type.algorithmic_features.B}"
213 --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
214 -W "${options_type.algorithmic_features.W}"
215 ${options_type.algorithmic_features.N}
216
217 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "True":
218 -S "${options_type.algorithmic_features.genotype_variant_threshold.S}"
219 #end if
220
221 ${options_type.algorithmic_features.j}
222 ${options_type.algorithmic_features.H}
223 -D "${options_type.algorithmic_features.D}"
224 ${options_type.algorithmic_features.genotype_qualities}
225 #end if
226 #end if
227
228 </command>
229
230 <inputs>
231 <conditional name="reference_source">
232 <param name="reference_source_selector" type="select" label="Load reference genome from">
233 <option value="cached">Local cache</option>
234 <option value="history">History</option>
235 </param>
236 <when value="cached">
237 <repeat name="input_bams" title="Sample BAM file" min="1">
238 <param name="input_bam" type="data" format="bam" label="BAM file">
239 <validator type="unspecified_build" />
240 <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." />
241 </param>
242 </repeat>
243
244 <param name="ref_file" type="select" label="Using reference genome">
245 <options from_data_table="fasta_indexes"></options>
246 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
247 </param>
248 </when>
249 <when value="history"> <!-- FIX ME!!!! -->
250 <repeat name="input_bams" title="Sample BAM file" min="1">
251 <param name="input_bam" type="data" format="bam" label="BAM file" />
252 </repeat>
253 <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" />
254 </when>
255 </conditional>
256
257 <conditional name="target_limit_type">
258 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
259 <option value="do_not_limit" selected="True">Do not limit</option>
260 <option value="limit_by_target_file">Limit by target file</option>
261 <option value="limit_by_region">Limit to region</option>
262 </param>
263 <when value="do_not_limit">
264 <!-- Do nothing here -->
265 </when>
266 <when value="limit_by_target_file">
267 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/>
268 </when>
269 <when value="limit_by_region">
270 <param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? -->
271 <param name="region_start" type="integer" label="Region Start" value="" />
272 <param name="region_end" type="integer" label="Region End" value="" />
273 </when>
274 </conditional>
275
276 <conditional name="options_type">
277 <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need" >
278 <option value="simple" selected="True">1:Simple diploid calling</option>
279 <option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option>
280 <option value="naive">3:Frequency-based pooled calling</option>
281 <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
282 <option value="full">5:Complete list of all options</option>
283 <!-- We will not alloow command line text boxes at this time
284 <option value="cline">6:Input parameters on the command line</option>
285 -->
286 </param>
287 <when value="full">
288
289 <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" /> 290 <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"> 291 <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" /> 292 <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"/> 293 <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"/> 294 <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." /> 315 <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> 316 </when>
270 <when value="do_not_set"> 317 <when value="do_not_set">
271 <!-- do nothing --> 318 <!-- do nothing -->
272 </when> 319 </when>
273 </conditional> 320 </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 -->
337 321
338 <!-- reporting --> 322 <!-- reporting -->
339 323
340 <conditional name="reporting"> 324 <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" /> 325 <param name="reporting_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set reporting option?" help="Sets -P --pvar option" />
366 350
367 <conditional name="reference_allele"> 351 <conditional name="reference_allele">
368 <param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options " /> 352 <param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options " />
369 <when value="set"> 353 <when value="set">
370 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" help="-Z --use-reference-allele; default=False" /> 354 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" help="-Z --use-reference-allele; default=False" />
371 <param name="reference_quality" type="text" size="8" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60 " /> 355 <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60 " />
372 </when> 356 </when>
373 <when value="do_not_set"> 357 <when value="do_not_set">
374 <!-- do nothing --> 358 <!-- do nothing -->
375 </when> 359 </when>
376 </conditional> 360 </conditional>
469 <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak algorithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " /> 453 <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak algorithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " />
470 <when value="set"> 454 <when value="set">
471 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" /> 455 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" />
472 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." /> 456 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
473 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" help="--genotyping-max-banddepth; default=6" /> 457 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" help="--genotyping-max-banddepth; default=6" />
474 <param name="W" type="text" size="8" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" /> 458 <param name="W" type="text" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" />
475 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" help="-N --exclude-unobserved-genotypes; default=False" /> 459 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" help="-N --exclude-unobserved-genotypes; default=False" />
476 <conditional name="genotype_variant_threshold"> 460 <conditional name="genotype_variant_threshold">
477 <param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" /> 461 <param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" />
478 <when value="do_not_set"> 462 <when value="do_not_set">
479 <!-- do nothing --> 463 <!-- do nothing -->
504 </when> 488 </when>
505 <when value="naive_w_filters"> 489 <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--> 490 <!-- 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 " /> 491 <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> 492 </when>
493 </conditional>
494
495 </inputs>
509 496
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> 497 <outputs>
532 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> 498 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
533 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> 499 <data format="bed" name="output_failed_alleles_bed" label="${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> 500 <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> 501 </data>
543 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> 509 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
544 <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/> 510 <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
545 <param name="options_type_selector" value="simple"/> 511 <param name="options_type_selector" value="simple"/>
546 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/> 512 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
547 </test> 513 </test>
514 <test>
515 <param name="reference_source_selector" value="history" />
516 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
517 <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
518 <param name="options_type_selector" value="naive_w_filters"/>
519 <param name="min_coverage" value="14"/>
520 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
521 </test>
548 </tests> 522 </tests>
549 <stdio> 523 <stdio>
550 <exit_code range="1:" /> 524 <exit_code range="1:" />
551 </stdio> 525 </stdio>
552 <help> 526 <help>
554 528
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. 529 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.
556 530
557 See https://github.com/ekg/freebayes for details on FreeBayes. 531 See https://github.com/ekg/freebayes for details on FreeBayes.
558 532
559 This Galaxy instance of FreeBayes corresponds to release 0.9.18 533 This Galaxy instance of FreeBayes corresponds to release 0.9.20
560 534
561 ------ 535 ------
562 536
563 **Description** 537 **Description**
564 538