comparison freebayes.xml @ 25:bf27106652f3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

24:da6e10dee68b

<tool id="freebayes" name="FreeBayes" version="1.0.2.29--1">
    <description> - bayesian genetic variant detector</description>
    <requirements>
        <requirement type="package" version="1.0.2.29">freebayes</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="4.1.3">gawk</requirement>
        <requirement type="package" version="20160622">parallel</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
<![CDATA[
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s -f "${reference_source.ref_file}" "${reference_fasta_filename}" &&
        samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        ln -s -f "${input_bam}" "b_${bam_count}.bam" &&
        ln -s -f "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&
    #end for

    ## Tabixize optional input_varinat_vcf file (for --variant-input option)
    #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
        ln -s -f "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&
        ln -s -f "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&
    #end if

    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
    #end for

    sort -u regions_all.bed > regions_uniq.bed &&
    ## split into even small chunks, this has some disatvantages and will not be used for the moment
    ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&

    ## Finished setting up inputs

    for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
    do

    echo "

    ## COMMAND LINE STARTS HERE

    freebayes

    --region '\$i'

    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        --bam 'b_${bam_count}.bam'
    #end for
    --fasta-reference '${reference_fasta_filename}'

    ## Outputs
    --vcf './vcf_output/part_\$i.vcf'

    #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
        --targets '${target_limit_type.input_target_bed}'
    #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
        --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
    #end if

    ##advanced options
    #if str( $options_type.options_type_selector ) == "simple":
        ##do nothing as command like build up to this point is sufficinet for simple diploid calling

    #elif str( $options_type.options_type_selector ) == "simple_w_filters":
        --standard-filters
        --min-coverage '${options_type.min_coverage}'
    #elif str( $options_type.options_type_selector ) == "naive":
        --haplotype-length 0
        --min-alternate-count 1
        --min-alternate-fraction 0
        --pooled-continuous
        --report-monomorphic
    #elif str( $options_type.options_type_selector ) == "naive_w_filters":
        --haplotype-length 0
        --min-alternate-count 1
        --min-alternate-fraction 0
        --pooled-continuous
        --report-monomorphic
        --standard-filters
        --min-coverage '${options_type.min_coverage}'

    ## Command line direct text entry is not allowed at this time for security reasons
    #elif str( $options_type.options_type_selector ) == "full":
        #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
            ${options_type.optional_inputs.report_monomorphic}

            #if $options_type.optional_inputs.output_trace_option:
                --trace ./trace/part_'\$i'.txt
            #end if
            #if $options_type.optional_inputs.output_failed_alleles_option:
                --failed-alleles ./failed_alleles/part_'\$i'.bed
            #end if
            #if $options_type.optional_inputs.samples:
                --samples '${options_type.optional_inputs.samples}'
            #end if
            #if $options_type.optional_inputs.populations:
                --populations '${options_type.optional_inputs.populations}'
            #end if
            #if $options_type.optional_inputs.A:
                --cnv-map '${options_type.optional_inputs.A}'
            #end if
            #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
                --variant-input 'input_variant_vcf.vcf.gz'  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
                ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
            #end if
            #if $options_type.optional_inputs.haplotype_basis_alleles:
                --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
            #end if
            #if $options_type.optional_inputs.observation_bias:
                --observation-bias '${options_type.optional_inputs.observation_bias}'
            #end if
            #if $options_type.optional_inputs.contamination_estimates:
                --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
            #end if
        #end if

    ## REPORTING
        #if str( $options_type.reporting.reporting_selector ) == "set":
            --pvar ${options_type.reporting.pvar}
        #end if
    ## POPULATION MODEL
        #if str( $options_type.population_model.population_model_selector ) == "set":
            --theta '${options_type.population_model.T}'
            --ploidy '${options_type.population_model.P}'
            ${options_type.population_model.J}
            ${options_type.population_model.K}
        #end if

    ## REFERENCE ALLELE
        #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
            ${options_type.reference_allele.Z}
            --reference-quality '${options_type.reference_allele.reference_quality}'
        #end if

    ## ALLELE SCOPE
        #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
            ${options_type.allele_scope.I}
            ${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
        ${options_type.O}

    ##INPUT FILTERS
        #if str( $options_type.input_filters.input_filters_selector ) == "set":
            ${options_type.input_filters.use_duplicate_reads}
            -m '${options_type.input_filters.m}'
            -q '${options_type.input_filters.q}'
            -R '${options_type.input_filters.R}'
            -Y '${options_type.input_filters.Y}'

            #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
              -Q '${options_type.input_filters.mismatch_filters.Q}'
              -U '${options_type.input_filters.mismatch_filters.U}'
              -z '${options_type.input_filters.mismatch_filters.z}'
              --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
            #end if

            -e '${options_type.input_filters.e}'
            -F '${options_type.input_filters.F}'
            -C '${options_type.input_filters.C}'
            --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
            -G '${options_type.input_filters.G}'
            --min-coverage '${options_type.input_filters.min_coverage}'
        #end if

    ## POPULATION AND MAPPABILITY PRIORS
        #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
            ${options_type.population_mappability_priors.k}
            ${options_type.population_mappability_priors.w}
            ${options_type.population_mappability_priors.V}
            ${options_type.population_mappability_priors.a}
        #end if

    ## GENOTYPE LIKELIHOODS
        #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
          --base-quality-cap '${$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 ) == "set":
            ${options_type.algorithmic_features.report_genotype_likelihood_max}
            -B '${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}

            #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
                -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
            #end if

            ${options_type.algorithmic_features.j}
            ${options_type.algorithmic_features.H}
            -D '${options_type.algorithmic_features.D}'
            ${options_type.algorithmic_features.genotype_qualities}
        #end if
    #end if

    ";
    done > freebayes_commands.sh &&
    cat freebayes_commands.sh | parallel --no-notice -j \${GALAXY_SLOTS:-1} &&

    ## make VCF header

    grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&

    for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
    do
        ## if this fails then it bails out the script
        cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
        ;
    done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > "${output_vcf}"

    #if str( $options_type.options_type_selector ) == "full":
        #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
            #if $options_type.optional_inputs.output_failed_alleles_option:
                &&

                    ;
                done > '${output_trace}'
            #end if
        #end if
    #end if
]]>
    </command>

    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Load reference genome from">
                <option value="cached">Local cache</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
                    <validator type="unspecified_build" />

                </param>
            </when>
            <when value="history"> <!-- FIX ME!!!! -->
                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
                <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" />
            </when>
        </conditional>
        <conditional name="target_limit_type">
            <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
                <option value="do_not_limit" selected="True">Do not limit</option>
                <option value="limit_by_target_file">Limit by target file</option>
                <option value="limit_by_region">Limit to region</option>
            </param>
            <when value="do_not_limit">
                <!-- Do nothing here -->
            </when>
            <when value="limit_by_target_file">
                <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/>
            </when>
            <when value="limit_by_region">
                <param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? -->
                <param name="region_start" type="integer" label="Region Start" value="" />
                <param name="region_end" type="integer" label="Region End" value="" />
            </when>
        </conditional>
        <conditional name="options_type">
            <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need" >
                <option value="simple" selected="True">1:Simple diploid calling</option>
                <option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option>
                <option value="naive">3:Frequency-based pooled calling</option>
                <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
                <option value="full">5:Complete list of all options</option>
                <!-- We will not alloow command line text boxes at this time
                <option value="cline">6:Input parameters on the command line</option>
                -->
            </param>
            <when value="full">
                <conditional name="optional_inputs">
                    <param name="optional_inputs_selector" type="select" label="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">
                        <option value="do_not_set" selected="true">Do not provide additional inputs</option>
                        <option value="set">Provide additional inputs</option>
                    </param>
                    <when value="set">
                        <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False"
                            label="Write out failed alleles file" help="--failed-alleles" />
                        <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
                            label="Write out algorithm trace file" help="--trace"/>
                        <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"/>
                        <param name="populations" type="data" format="txt" label="Populations File" optional="True"
                            help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of.
                            The population-based bayesian inference model will then be partitioned on the basis of the populations" />
                        <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
                            help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format:
                            reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/>
                        <conditional name="input_variant_type">
                            <param name="input_variant_type_selector" type="select" label="Provide variants file">
                                <option value="do_not_provide" selected="True">Do not provide</option>
                                <option value="provide_vcf">Provide VCF file</option>
                            </param>
                            <when value="do_not_provide">
                                <!-- Do nothing here -->
                            </when>
                            <when value="provide_vcf">
                                <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm">
                                    <conversion name="Tabixized_input" type="tabix" />
                                </param>
                                <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
                            </when>
                        </conditional>
                        <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True"
                            help="--haplotype-basis-alleles" />
                        <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False"
                            label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes."
                            help="--report-monomorphic  " />
                        <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
                            help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
                        <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." />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
                <!-- reporting -->
                <conditional name="reporting">
                  <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
                        <option value="do_not_set" selected="True">Use defaults</option>
                        <option value="set">Set reporting options</option>
                  </param>
                  <when value="set">
                    <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than"
                        help="-P --pvar; default=0.0. Note that post-filtering is generally recommended over the use of this parameter.  " />
                  </when>
                  <when value="do_not_set">
                    <!-- do nothing -->
                  </when>
                </conditional>
                <!-- population model -->
                <conditional name="population_model">
                    <param name="population_model_selector" type="select" label="Population model options"
                        help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options  " >
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set population model options</option>
                    </param>
                    <when value="set">
                        <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
                            help="-T --theta; default = 0.001. This serves as the single parameter to the Ewens Sampling Formula prior model." />
                        <param name="P" type="integer" value="2" label="Set ploidy for the analysis" help="-p --ploidy; default=2" />
                        <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
                            help="-J --pooled-discrete; default=False. Model pooled samples using discrete genotypes across pools.
                            When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy." />
                        <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"
                            help="-K, --poled-continuous; default=False." />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
                <!-- reference allele -->
                <conditional name="reference_allele">
                    <param name="reference_allele_selector" type="select" label="Reference allele options"
                        help="Sets --use-reference-allele and --reference-quality options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set reference allele options</option>
                    </param>
                    <when value="set">
                        <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" />
                        <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  " />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
                <!-- allelic scope -->
                <conditional name="allele_scope">
                    <param name="allele_scope_selector" type="select" label="Allelic scope options"
                        help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set alleic scope options</option>
                    </param>
                    <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>
                <!-- indel realignment -->
                <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels?"
                    help="-O --dont-left-align-indels; default=False (do left align)." />
                <!-- input filters -->
                <conditional name="input_filters">
                    <param name="input_filters_selector" type="select" label="Input filters"
                        help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
                        <option value="do_not_set" selected="true">No input filters (default)</option>
                        <option value="set">Set input filters</option>
                    </param>
                    <when value="set">  
                        <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False"
                            label="Include duplicate-marked alignments in the analysis."
                            help="-4 --use-duplicate-reads; default=False (exclude duplicates marked as such in alignments)." />
                        <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
                            help="-m --min-mapping-quality; default=1" />
                        <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
                            help="-q --min-base-quality; default=0" />
                        <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"
                            help="-R --min-supporting-allele-qsum; default=0" />
                        <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"
                            help="-Y --min-supporting-mapping-qsum; default=0" />
                        <conditional name="mismatch_filters">
                            <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
                                help="Sets -Q, -U, -z, and &#36; options">
                                <option value="do_not_set" selected="true">No mismatch filters (default)</option>
                                <option value="set">Set mismatch filters</option>
                            </param>
                            <when value="set">
                                <param name="Q" type="integer" value="10" label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
                                    help="-Q --mismatch-base-quality-threshold; default=10" />
                                <param name="U" type="integer" value="1000" optional="True" label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
                                    help="-U --read-mismatch-limit; default=~unbound" />
                                <param name="z" type="float" value="1.0" min="0.0" max="1.0"
                                    label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)"
                                    help="-z --read-max-mismatch-fraction; default=1.0" />
                                <param name="read_snp_limit" type="integer"
                                    value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
                                    help="-$amp; --read-snp-limit N " />
                            </when>
                            <when value="do_not_set">
                                <!-- do nothing -->
                            </when>
                        </conditional>
                        <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
                            help="-e --read-snp-limit; default=~unbounded" />
                        <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False" label="Use stringent input base and mapping quality filters"
                            help="-0 --standard-filters; default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" />
                        <param name="F" type="float" value="0.2"
                            label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"
                            help="-F --min-alternate-fraction; default=0.2" />
                        <param name="C" type="integer" value="2"
                            label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
                            help="-C --min-alternate-count; default=2" />
                        <param name="min_alternate_qsum" type="integer" value="0"
                            label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"
                            help="-3 --min-alternate-qsum; default=0" />
                        <param name="G" type="integer" value="1"
                            label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"
                            help="-G --min-alternate-total N; default=1" />
                        <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site"
                            help="-! --min-coverage; default=0  " />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
                <!-- population and mappability priors -->
                <conditional name="population_mappability_priors">
                    <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
                        help="Sets -k, -w, -V, and -a options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set population and mappability priors</option>
                    </param>
                    <when value="set">
                        <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
                            help="-k --no-population-priors; default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors." />
                        <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False"
                            label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
                            help="-w --hwe-priors-off; default=False" />
                        <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
                            help="-V --binomial-obs-priors-off; default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability." />
                        <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False"
                            label="isable use of aggregate probability of observation balance between alleles as a component of the priors"
                            help="-a --allele-balance-priors-off; default=False  " />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                  </conditional>
                <!-- genotype likelihoods -->
                <conditional name="genotype_likelihoods">
                    <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
                        help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set genotype likelihood options</option>
                    </param>
                    <when value="set">
                        <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at" help="--base-quality-cap" />
                        <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False"
                            label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
                            help="--experimental-gls; Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples." />
                        <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
                            help="--prob-contamination; default=10e-9." />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
                <!-- algorithmic features -->
                <conditional name="algorithmic_features">
                    <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
                        help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set algorithmic features</option>
                    </param>
                    <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" 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" />
                        <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" />
                        <conditional name="genotype_variant_threshold">
                            <param name="genotype_variant_threshold_selector" type="select"
                                label="Limit posterior integration"
                                help="-S --genotype-variant-threshold">
                                <option value="do_not_set" selected="true">Do not limit posterior integration</option>
                                <option value="set">Set posterior integration limit</option>
                            </param>
                            <when value="do_not_set">
                                <!-- do nothing -->
                            </when>
                            <when value="set">
                                <param name="S" value="" type="integer"
                                    label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample."
                                    help="-S --genotype-variant-threshold; default=~unbounded" />
                            </when>
                        </conditional>
                        <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods"
                            help="-j --use-mapping-quality; default=False" />
                        <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False"
                            label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
                            help="-H --harmonic-indel-quality; default=use a minimum Base Quality in flanking sequence." />
                        <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"
                            help="-D --read-dependence-factor; default=0.9." />
                        <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False"
                            label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
                            help="-= --genotype-qualities; default=False  " />
                    </when>
                    <when value="do_not_set">
                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
            <when value="simple">
                <!-- do nothing -->
            </when>
            <when value="simple_w_filters">
                <!-- add standard-filters to command line -->
            <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0  " />
            </when>
            <when value="naive">
                <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
            </when>
            <when value="naive_w_filters">
                <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
                <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0  " />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />

-------

**Galaxy-specific options**

Galaxy allows six levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:

 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage. 
 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes. 
 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.

-----

                   each sample field in the VCF output.


------

**Citation**

For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_.

The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
TNG was developed by Bjoern Gruening

    </help>
    <citations>
        <citation type="bibtex">@misc{1207.3907,
Author = {Erik Garrison},
Title = {Haplotype-based variant detection from short-read sequencing},
Year = {2012},
Eprint = {arXiv:1207.3907},
url = {http://arxiv.org/abs/1207.3907},
}</citation>
    </citations>
</tool>

25:bf27106652f3

<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2">
    <description>bayesian genetic variant detector</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="4.1.3">gawk</requirement>
        <requirement type="package" version="20160622">parallel</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
        samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
        ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
    #end for

    ## Tabixize optional input_variant_vcf file (for --variant-input option)
    #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
        ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' &&
        ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
    #end if

    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        samtools view -H b_${bam_count}.bam |
        grep "^@SQ" |
        cut -f 2- |
        awk '{ gsub("^SN:","",$1);
        gsub("^LN:","",$2);
        print $1"\t0\t"$2; }' >> regions_all.bed &&
    #end for

    sort -u regions_all.bed > regions_uniq.bed &&
    ## split into even small chunks, this has some disatvantages and will not be used for the moment
    ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&

    ## Finished setting up inputs

    for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
    do

        echo "

        ## COMMAND LINE STARTS HERE

        freebayes

        --region '\$i'

        #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
            --bam 'b_${bam_count}.bam'
        #end for
        --fasta-reference '${reference_fasta_filename}'

        ## Outputs
        --vcf './vcf_output/part_\$i.vcf'

        #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
            --targets '${target_limit_type.input_target_bed}'
        #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
            --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
        #end if

        ##advanced options
        #if str( $options_type.options_type_selector ) == "simple":
            ##do nothing as command like build up to this point is sufficinet for simple diploid calling

        #elif str( $options_type.options_type_selector ) == "simple_w_filters":
            --standard-filters
            --min-coverage '${options_type.min_coverage}'
        #elif str( $options_type.options_type_selector ) == "naive":
            --haplotype-length 0
            --min-alternate-count 1
            --min-alternate-fraction 0
            --pooled-continuous
            --report-monomorphic
        #elif str( $options_type.options_type_selector ) == "naive_w_filters":
            --haplotype-length 0
            --min-alternate-count 1
            --min-alternate-fraction 0
            --pooled-continuous
            --report-monomorphic
            --standard-filters
            --min-coverage '${options_type.min_coverage}'

        ## Command line direct text entry is not allowed at this time for security reasons
        #elif str( $options_type.options_type_selector ) == "full":
            #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
                ${options_type.optional_inputs.report_monomorphic}

                #if $options_type.optional_inputs.output_trace_option:
                    --trace ./trace/part_'\$i'.txt
                #end if
                #if $options_type.optional_inputs.output_failed_alleles_option:
                    --failed-alleles ./failed_alleles/part_'\$i'.bed
                #end if
                #if $options_type.optional_inputs.samples:
                    --samples '${options_type.optional_inputs.samples}'
                #end if
                #if $options_type.optional_inputs.populations:
                    --populations '${options_type.optional_inputs.populations}'
                #end if
                #if $options_type.optional_inputs.A:
                    --cnv-map '${options_type.optional_inputs.A}'
                #end if
                #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
                    --variant-input 'input_variant_vcf.vcf.gz'  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
                    ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
                #end if
                #if $options_type.optional_inputs.haplotype_basis_alleles:
                    --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
                #end if
                #if $options_type.optional_inputs.observation_bias:
                    --observation-bias '${options_type.optional_inputs.observation_bias}'
                #end if
                #if $options_type.optional_inputs.contamination_estimates:
                    --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
                #end if
            #end if

        ## REPORTING
            #if str( $options_type.reporting.reporting_selector ) == "set":
                --pvar ${options_type.reporting.pvar}
            #end if
        ## POPULATION MODEL
            #if str( $options_type.population_model.population_model_selector ) == "set":
                --theta '${options_type.population_model.T}'
                --ploidy '${options_type.population_model.P}'
                ${options_type.population_model.J}
                ${options_type.population_model.K}
            #end if

        ## REFERENCE ALLELE
            #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
                ${options_type.reference_allele.Z}
                --reference-quality '${options_type.reference_allele.reference_quality}'
            #end if

        ## ALLELE SCOPE
            #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
                ${options_type.allele_scope.I}
                ${options_type.allele_scope.i}
                ${options_type.allele_scope.X}
                ${options_type.allele_scope.u}
                ${options_type.allele_scope.no_partial_observations}

                -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}'
            #end if

        ## REALIGNMENT
            ${options_type.O}

        ##INPUT FILTERS
            #if str( $options_type.input_filters.input_filters_selector ) == "set":
                ${options_type.input_filters.use_duplicate_reads}
                -m '${options_type.input_filters.m}'
                -q '${options_type.input_filters.q}'
                -R '${options_type.input_filters.R}'
                -Y '${options_type.input_filters.Y}'
                -e '${options_type.input_filters.e}'
                -F '${options_type.input_filters.F}'
                -C '${options_type.input_filters.C}'
                -G '${options_type.input_filters.G}'

                #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
                  -Q '${options_type.input_filters.mismatch_filters.Q}'
                  -U '${options_type.input_filters.mismatch_filters.U}'
                  -z '${options_type.input_filters.mismatch_filters.z}'

                  --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
                #end if

                --min-coverage '${options_type.input_filters.min_coverage}'
                --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
            #end if

        ## POPULATION AND MAPPABILITY PRIORS
            #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
                ${options_type.population_mappability_priors.k}
                ${options_type.population_mappability_priors.w}
                ${options_type.population_mappability_priors.V}
                ${options_type.population_mappability_priors.a}
            #end if

        ## GENOTYPE LIKELIHOODS
            #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
              ${$options_type.genotype_likelihoods.experimental_gls}

              --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
              --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}'
            #end if

        ## ALGORITHMIC FEATURES
            #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
                -B '${options_type.algorithmic_features.B}'
                -W '${options_type.algorithmic_features.W}'
                -D '${options_type.algorithmic_features.D}'

                #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
                    -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
                #end if

                ${options_type.algorithmic_features.N}
                ${options_type.algorithmic_features.j}
                ${options_type.algorithmic_features.H}
                ${options_type.algorithmic_features.genotype_qualities}
                ${options_type.algorithmic_features.report_genotype_likelihood_max}

                --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}'
            #end if
        #end if

        ";
    done > freebayes_commands.sh &&

    cat freebayes_commands.sh |
    parallel --no-notice -j \${GALAXY_SLOTS:-1} &&

    ## make VCF header
    grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&

    for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
    do
        ## if this fails then it bails out the script
        cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
        ;
    done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'

    #if str( $options_type.options_type_selector ) == "full":
        #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
            #if $options_type.optional_inputs.output_failed_alleles_option:
                &&

                    ;
                done > '${output_trace}'
            #end if
        #end if
    #end if
    ]]></command>

    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
                    <validator type="unspecified_build" />

                </param>
            </when>
            <when value="history"> <!-- FIX ME!!!! -->
                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
                <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" />
            </when>
        </conditional>
        <conditional name="target_limit_type">
            <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
                <option value="do_not_limit" selected="True">Do not limit</option>
                <option value="limit_by_target_file">Limit by target file</option>
                <option value="limit_by_region">Limit to region</option>
            </param>
            <when value="do_not_limit" /><!-- Do nothing here -->
            <when value="limit_by_target_file">
                <param name="input_target_bed" type="data" format="bed" label="Limit analysis to regions in a file (BED-format)." argument="--targets"/>
            </when>
            <when value="limit_by_region">
                <param name="region_chromosome" type="text" label="Region Chromosome" value="" argument="--region"/> <!--only once? -->
                <param name="region_start" type="integer" label="Region Start" value="" />
                <param name="region_end" type="integer" label="Region End" value="" />
            </when>
        </conditional>
        <conditional name="options_type">
            <param name="options_type_selector" type="select" label="Choose parameter selection level"
                help="Select how much control over the freebayes run you need" >
                <option value="simple" selected="True">1. Simple diploid calling</option>
                <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
                <option value="naive">3. Frequency-based pooled calling</option>
                <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
                <option value="full">5. Full list of options</option>
            </param>
            <when value="full">
                <conditional name="optional_inputs">
                    <param name="optional_inputs_selector" type="select" label="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">
                        <option value="do_not_set" selected="true">Do not provide additional inputs</option>
                        <option value="set">Provide additional inputs</option>
                    </param>
                    <when value="set">
                        <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False"
                               label="Write out failed alleles file" argument="--failed-alleles" />
                        <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
                               label="Write out algorithm trace file" argument="--trace"/>
                        <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True"
                               help="default=By default FreeBayes will analyze all samples in its input BAM files" argument="--samples"/>
                        <param name="populations" type="data" format="txt" label="Populations File" optional="True"
                               help="Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will
                                     then be partitioned on the basis of the populations. [default=False]"
                               argument="--populations" />
                        <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
                               help="default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format:
                                     reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."
                               argument="--cnv-map" />
                        <conditional name="input_variant_type">
                            <param name="input_variant_type_selector" type="select" label="Provide variants file">
                                <option value="do_not_provide" selected="True">Do not provide</option>
                                <option value="provide_vcf">Provide VCF file</option>
                            </param>
                            <when value="do_not_provide" /><!-- Do nothing here -->
                            <when value="provide_vcf">
                                <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm" argument="--variant-input">
                                    <conversion name="Tabixized_input" type="tabix" />
                                </param>
                                <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False"
                                       label="Only provide variant calls and genotype likelihoods for sites in VCF" argument="--only-use-input-alleles" />
                            </when>
                        </conditional>
                        <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True"
                               argument="--haplotype-basis-alleles" />
                        <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False"
                               label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes."
                               argument="--report-monomorphic" />
                        <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
                               help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias"
                               argument="--observation-bias" />
                        <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from"
                               help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates."
                               argument="--contamination-estimates" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- reporting -->
                <conditional name="reporting">
                    <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
                        <option value="do_not_set" selected="True">Use defaults</option>
                        <option value="set">Set reporting options</option>
                    </param>
                    <when value="set">
                        <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than"
                               help="Note that post-filtering is generally recommended over the use of this parameter. [default=0.0]"
                               argument="--pvar" />
                  </when>
                  <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- population model -->
                <conditional name="population_model">
                    <param name="population_model_selector" type="select" label="Population model options"
                        help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options  " >
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set population model options</option>
                    </param>
                    <when value="set">
                        <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
                               help="This serves as the single parameter to the Ewens Sampling Formula prior model. [default = 0.001]" argument='--theta'/>
                        <param name="P" type="integer" value="2" label="Set ploidy for the analysis"
                               help="default=2" argument='--ploidy' />
                        <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
                               help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy. [default=False]"
                               argument="--pooled-discrete"/>
                        <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"
                               help="default=False." argument="--poled-continuous" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- reference allele -->
                <conditional name="reference_allele">
                    <param name="reference_allele_selector" type="select" label="Reference allele options"
                        help="Sets --use-reference-allele and --reference-quality options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set reference allele options</option>
                    </param>
                    <when value="set">
                        <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="default=False" argument="--use-reference-allele" />
                        <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="default=100,60" argument="--reference-quality" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- allelic scope -->
                <conditional name="allele_scope">
                    <param name="allele_scope_selector" type="select" label="Allelic scope options"
                        help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set alleic scope options</option>
                    </param>
                    <when value="set">
                        <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles"
                               help="default=False" argument="--no-snps" />
                        <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles"
                               help="default=False" argument="--no-indels" />
                        <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs"
                               help="default=False" argument="--no-mnps" />
                        <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
                               help="default=False" argument="--no-complex" />
                        <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate"
                               help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all. [default=0 (all)]"
                               argument="--use-best-n-alleles" />
                        <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="default=5." argument="--min-repeat-size" />
                        <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="default=0 (off)." argument="--min-repeat-entropy" />
                        <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="default=use all observations, dividing partial support across matching haplotypes when generating haplotypes."
                               argument="--no-partial-observations" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- indel realignment -->
                <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels"
                       help="default=False (do left align)." argument="--dont-left-align-indels" />

                <!-- input filters -->
                <conditional name="input_filters">
                    <param name="input_filters_selector" type="select" label="Input filters"
                           help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
                        <option value="do_not_set" selected="true">No input filters (default)</option>
                        <option value="set">Set input filters</option>
                    </param>
                    <when value="set">
                        <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False"
                               label="Include duplicate-marked alignments in the analysis."
                               help="default=False (exclude duplicates marked as such in alignments)." argument="--use-duplicate-reads" />
                        <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
                               help="default=1" argument="--min-mapping-quality" />
                        <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
                               help="default=0" argument="--min-base-quality" />
                        <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"
                               help="default=0" argument="--min-supporting-allele-qsum" />
                        <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"
                               help="default=0" argument="--min-supporting-mapping-qsum" />
                        <conditional name="mismatch_filters">
                            <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
                                   help="Sets -Q, -U, -z, and &#36; options">
                                <option value="do_not_set" selected="true">No mismatch filters (default)</option>
                                <option value="set">Set mismatch filters</option>
                            </param>
                            <when value="set">
                                <param name="Q" type="integer" value="10"
                                       label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
                                       help="default=10" argument="--mismatch-base-quality-threshold" />
                                <param name="U" type="integer" value="1000" optional="True"
                                       label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
                                       help="default=~unbound" argument="--read-mismatch-limit" />
                                <param name="z" type="float" value="1.0" min="0.0" max="1.0"
                                       label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)"
                                       help="default=1.0" argument="--read-max-mismatch-fraction" />
                                <param name="read_snp_limit" type="integer"
                                       value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
                                       argument="--read-snp-limit" />
                            </when>
                            <when value="do_not_set" /><!-- do nothing -->
                        </conditional>
                        <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
                               help="default=~unbounded" argument="--read-snp-limit" />
                        <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False"
                               label="Use stringent input base and mapping quality filters"
                               help="default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" argument="--standard-filters"/>
                        <param name="F" type="float" value="0.2"
                               label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"
                               help="default=0.2" argument="--min-alternate-fraction" />
                        <param name="C" type="integer" value="2"
                               label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
                               help="default=2" argument="--min-alternate-count" />
                        <param name="min_alternate_qsum" type="integer" value="0"
                               label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"
                               help="default=0" argument="--min-alternate-qsum" />
                        <param name="G" type="integer" value="1"
                               label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"
                               help="default=1" argument="--min-alternate-total" />
                        <expand macro="par_min_cov" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- population and mappability priors -->
                <conditional name="population_mappability_priors">
                    <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
                        help="Sets -k, -w, -V, and -a options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set population and mappability priors</option>
                    </param>
                    <when value="set">
                        <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
                               help="default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors."
                               argument="--no-population-priors" />
                        <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False"
                               label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
                               help="default=False" argument="--hwe-priors-off" />
                        <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
                               help="default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability."
                               argument="--binomial-obs-priors-off" />
                        <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False"
                               label="Disable use of aggregate probability of observation balance between alleles as a component of the priors"
                               help="default=False"
                               argument="--allele-balance-priors-off" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                  </conditional>

                <!-- genotype likelihoods -->
                <conditional name="genotype_likelihoods">
                    <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
                           help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options.">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set genotype likelihood options</option>
                    </param>
                    <when value="set">
                        <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at"
                               argument="--base-quality-cap" />
                        <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False"
                               label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
                               help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples."
                               argument="--experimental-gls" />
                        <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
                               help="default=10e-9." argument="--prob-contamination" />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>

                <!-- algorithmic features -->
                <conditional name="algorithmic_features">
                    <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
                           help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
                        <option value="do_not_set" selected="true">Use defaults</option>
                        <option value="set">Set algorithmic features</option>
                    </param>
                    <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="default=False" argument="--report-genotype-likelihood-max" />
                        <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
                               help="default=1000." argument="--genotyping-max-iterations" />
                        <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping"
                               help="default=6" argument="--genotyping-max-banddepth" />
                        <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="default=1,3" argument="--posterior-integration-limits" />
                        <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="default=False" argument="--exclude-unobserved-genotypes" />
                        <conditional name="genotype_variant_threshold">
                            <param name="genotype_variant_threshold_selector" type="select"
                                   label="Limit posterior integration" argument="--genotype-variant-threshold">
                                <option value="do_not_set" selected="true">Do not limit posterior integration</option>
                                <option value="set">Set posterior integration limit</option>
                            </param>
                            <when value="do_not_set" /><!-- do nothing -->
                            <when value="set">
                                <param name="S" value="" type="integer"
                                       label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample."
                                       help="default=~unbounded" argument="--genotype-variant-threshold" />
                            </when>
                        </conditional>
                        <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False"
                               label="Use mapping quality of alleles when calculating data likelihoods"
                               help="default=False" argument="--use-mapping-quality" />
                        <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False"
                               label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
                               help="default=use a minimum Base Quality in flanking sequence." argument="--harmonic-indel-quality" />
                        <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"
                               help="default=0.9." argument="--read-dependence-factor" />
                        <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False"
                               label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
                               help="-= --genotype-qualities; default=False  " />
                    </when>
                    <when value="do_not_set" /><!-- do nothing -->
                </conditional>
            </when>
            <when value="simple" /><!-- do nothing -->
            <when value="simple_w_filters">
                <!-- add standard-filters to command line -->
                <expand macro="par_min_cov" />
            </when>
            <when value="naive">
                <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
            </when>
            <when value="naive_w_filters">
                <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
                <expand macro="par_min_cov" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />

-------

**Galaxy-specific options**

Galaxy allows five levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:

 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage.
 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes.
 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.

-----

                   each sample field in the VCF output.


------

**Acknowledgments**

The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
TNG was developed by Bjoern Gruening
    </help>
    <expand macro="citations" />
</tool>