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comparison freebayes.xml @ 15:59731e950e23 draft

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Fix some options.
author soranzo
date Fri, 29 Aug 2014 12:15:44 -0400
parents 2dd40b601766
children 6d9407020066
comparison
equal deleted inserted replaced
14:443ccd9208a0 15:59731e950e23
117 ${options_type.allele_scope.i} 117 ${options_type.allele_scope.i}
118 ${options_type.allele_scope.X} 118 ${options_type.allele_scope.X}
119 ${options_type.allele_scope.u} 119 ${options_type.allele_scope.u}
120 -n "${options_type.allele_scope.n}" 120 -n "${options_type.allele_scope.n}"
121 --haplotype-length "${options_type.allele_scope.haplotype_length}" 121 --haplotype-length "${options_type.allele_scope.haplotype_length}"
122 --min-repeat-length "${options_type.allele_scope.min_repeat_length}" 122 --min-repeat-size "${options_type.allele_scope.min_repeat_length}"
123 --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}" 123 --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
124 ${options_type.allele_scope.no_partial_observations} 124 ${options_type.allele_scope.no_partial_observations}
125 #end if 125 #end if
126 126
127 ## REALIGNMENT 127 ## REALIGNMENT
164 ## GENOTYPE LIKELIHOODS 164 ## GENOTYPE LIKELIHOODS
165 165
166 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True": 166 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
167 --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}" 167 --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
168 ${$options_type.genotype_likelihoods.experimental_gls} 168 ${$options_type.genotype_likelihoods.experimental_gls}
169 --prob_contamination "${$options_type.genotype_likelihoods.prob_contamination}" 169 --prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}"
170 #end if 170 #end if
171 171
172 ## ALGORITHMIC FEATURES 172 ## ALGORITHMIC FEATURES
173 173
174 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True": 174 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
175 v 175 ${options_type.algorithmic_features.report_genotype_likelihood_max}
176 -B "${options_type.algorithmic_features.B}" 176 -B "${options_type.algorithmic_features.B}"
177 --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}" 177 --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
178 -W "${options_type.algorithmic_features.W}" 178 -W "${options_type.algorithmic_features.W}"
179 ${options_type.algorithmic_features.N} 179 ${options_type.algorithmic_features.N}
180 180
373 </conditional> 373 </conditional>
374 374
375 <!-- allelic scope --> 375 <!-- allelic scope -->
376 376
377 <conditional name="allele_scope"> 377 <conditional name="allele_scope">
378 <param name="allele_scope_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set allelic scope?" help="Sets -I, i, -X, -u, -n, -E, --haplotype-length, --min-repeat-length, --min-repeat-entropy, and --no-partial-observations options " /> 378 <param name="allele_scope_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set allelic scope?" help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options " />
379 <when value="set"> 379 <when value="set">
380 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" /> 380 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" />
381 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" /> 381 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" />
382 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" /> 382 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" />
383 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." help="-u --no-complex; default=False" /> 383 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." help="-u --no-complex; default=False" />
384 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate" help="-n --use-best-n-alleles; default=0 (all). Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" /> 384 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate" help="-n --use-best-n-alleles; default=0 (all). Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
385 <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" help="--haplotype-length; default=3." /> 385 <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" help="-E --max-complex-gap --haplotype-length; default=3." />
386 <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp" help="--min-repeat-length; default=5." /> 386 <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp" help="--min-repeat-size; default=5." />
387 <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" help="--min-repeat-entrpy; default=0 (off)." /> 387 <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" help="--min-repeat-entropy; default=0 (off)." />
388 <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False" label="Exclude observations which do not fully span the dynamically-determined detection window" help="--no-partial-observations; default=use all observations, dividing partial support across matching haplotypes when generating haplotypes. " /> 388 <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False" label="Exclude observations which do not fully span the dynamically-determined detection window" help="--no-partial-observations; default=use all observations, dividing partial support across matching haplotypes when generating haplotypes. " />
389 </when> 389 </when>
390 <when value="do_not_set"> 390 <when value="do_not_set">
391 <!-- do nothing --> 391 <!-- do nothing -->
392 </when> 392 </when>
461 </conditional> 461 </conditional>
462 462
463 <!-- algorithmic features --> 463 <!-- algorithmic features -->
464 464
465 <conditional name="algorithmic_features"> 465 <conditional name="algorithmic_features">
466 <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak agrithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " /> 466 <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 " />
467 <when value="set"> 467 <when value="set">
468 <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" /> 468 <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" />
469 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." /> 469 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
470 <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" /> 470 <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" />
471 <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" /> 471 <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" />
678 supporting quality scores. (Set to 0 to use all; default: all) 678 supporting quality scores. (Set to 0 to use all; default: all)
679 -E --max-complex-gap N 679 -E --max-complex-gap N
680 --haplotype-length N 680 --haplotype-length N
681 Allow haplotype calls with contiguous embedded matches of up 681 Allow haplotype calls with contiguous embedded matches of up
682 to this length. (default: 3) 682 to this length. (default: 3)
683 --min-repeat-length N 683 --min-repeat-size N
684 When assembling observations across repeats, require the total repeat 684 When assembling observations across repeats, require the total repeat
685 length at least this many bp. (default: 5) 685 length at least this many bp. (default: 5)
686 --min-repeat-entropy N 686 --min-repeat-entropy N
687 To detect interrupted repeats, build across sequence until it has 687 To detect interrupted repeats, build across sequence until it has
688 entropy > N bits per bp. (default: 0, off) 688 entropy > N bits per bp. (default: 0, off)