comparison freebayes.xml @ 15:59731e950e23 draft

Fix some options.

14:443ccd9208a0

            ${options_type.allele_scope.i}
            ${options_type.allele_scope.X}
            ${options_type.allele_scope.u}
            -n "${options_type.allele_scope.n}"
            --haplotype-length "${options_type.allele_scope.haplotype_length}"
            --min-repeat-length "${options_type.allele_scope.min_repeat_length}"
            --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
            ${options_type.allele_scope.no_partial_observations}
        #end if
        
## REALIGNMENT

## GENOTYPE LIKELIHOODS
        
        #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
          --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
          ${$options_type.genotype_likelihoods.experimental_gls}
          --prob_contamination "${$options_type.genotype_likelihoods.prob_contamination}"
        #end if
        
## ALGORITHMIC FEATURES
        
        #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
            v
            -B "${options_type.algorithmic_features.B}"
            --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
            -W "${options_type.algorithmic_features.W}"
            ${options_type.algorithmic_features.N}
            

      </conditional>

    <!-- allelic scope -->

      <conditional name="allele_scope">
        <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  " />
        <when value="set">
          <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" />
          <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" />
          <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" />
          <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." help="-u --no-complex; default=False" />
          <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" />
          <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." />
          <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." />
          <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)." />
          <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.  " />
        </when>
        <when value="do_not_set">
          <!-- do nothing -->
        </when>

    </conditional>
    
    <!-- algorithmic features -->
    
    <conditional name="algorithmic_features">
      <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  " />
      <when value="set">
        <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" />
        <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
        <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" />
        <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" />

                   supporting quality scores.  (Set to 0 to use all; default: all)
   -E --max-complex-gap N
      --haplotype-length N
                   Allow haplotype calls with contiguous embedded matches of up
                   to this length.  (default: 3)
   --min-repeat-length N
                   When assembling observations across repeats, require the total repeat
                   length at least this many bp.  (default: 5)
   --min-repeat-entropy N
                   To detect interrupted repeats, build across sequence until it has
                   entropy > N bits per bp.  (default: 0, off)

15:59731e950e23

            ${options_type.allele_scope.i}
            ${options_type.allele_scope.X}
            ${options_type.allele_scope.u}
            -n "${options_type.allele_scope.n}"
            --haplotype-length "${options_type.allele_scope.haplotype_length}"
            --min-repeat-size "${options_type.allele_scope.min_repeat_length}"
            --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
            ${options_type.allele_scope.no_partial_observations}
        #end if
        
## REALIGNMENT

## GENOTYPE LIKELIHOODS
        
        #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
          --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
          ${$options_type.genotype_likelihoods.experimental_gls}
          --prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}"
        #end if
        
## ALGORITHMIC FEATURES
        
        #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
            ${options_type.algorithmic_features.report_genotype_likelihood_max}
            -B "${options_type.algorithmic_features.B}"
            --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
            -W "${options_type.algorithmic_features.W}"
            ${options_type.algorithmic_features.N}
            

      </conditional>

    <!-- allelic scope -->

      <conditional name="allele_scope">
        <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  " />
        <when value="set">
          <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" />
          <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" />
          <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" />
          <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." help="-u --no-complex; default=False" />
          <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" />
          <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." />
          <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." />
          <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)." />
          <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.  " />
        </when>
        <when value="do_not_set">
          <!-- do nothing -->
        </when>

    </conditional>
    
    <!-- algorithmic features -->
    
    <conditional name="algorithmic_features">
      <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  " />
      <when value="set">
        <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" />
        <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
        <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" />
        <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" />

                   supporting quality scores.  (Set to 0 to use all; default: all)
   -E --max-complex-gap N
      --haplotype-length N
                   Allow haplotype calls with contiguous embedded matches of up
                   to this length.  (default: 3)
   --min-repeat-size N
                   When assembling observations across repeats, require the total repeat
                   length at least this many bp.  (default: 5)
   --min-repeat-entropy N
                   To detect interrupted repeats, build across sequence until it has
                   entropy > N bits per bp.  (default: 0, off)