annotate freebayes.xml @ 11:e9ebed0c12f6 draft

Check exit code instead of stderr, since FreeBayes writes warnings there (e.g. "Could not find any mapped reads in target region chr1:955302..955952"). Also document change of available options in FreeBayes >= 0.9.9.

<?xml version="1.0"?>
<tool id="freebayes" name="FreeBayes" version="0.0.3">
  <requirements>
    <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <description> - Bayesian genetic variant detector</description>
  <command>
    ##set up input files
    #set $reference_fasta_filename = "localref.fa"
    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
        samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if
    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
        ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
    #end for
    ##finished setting up inputs
    
    ##start FreeBayes commandline
    freebayes
    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
        --bam "localbam_${bam_count}.bam"
    #end for
    --fasta-reference "${reference_fasta_filename}" 
    
    ##outputs
    --vcf "${output_vcf}"
    
    ##advanced options
    #if str( $options_type.options_type_selector ) == "advanced":
        ##additional outputs
        #if $options_type.output_trace_option:
            --trace "${output_trace}"
        #end if
        #if $options_type.output_failed_alleles_option:
            --failed-alleles "${output_failed_alleles_bed}"
        #end if
        
        ##additional inputs
        #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
            --targets "${options_type.target_limit_type.input_target_bed}"
        #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region":
            --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}"
        #end if
        #if $options_type.input_sample_file:
            --samples "${options_type.input_sample_file}"
        #end if
        #if $options_type.input_populations_file:
            --populations "${options_type.input_populations_file}"
        #end if
        #if $options_type.input_cnv_map_bed:
            --cnv-map "${options_type.input_cnv_map_bed}"
        #end if
        #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":
            --variant-input "${options_type.input_variant_type.input_variant_vcf}"
            ${options_type.input_variant_type.only_use_input_alleles}
        #end if
        #if $options_type.haplotype_basis_alleles:
            --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}"
        #end if
        
        
        ##reporting
        #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":
            --pvar "${options_type.section_reporting_type.pvar}"
            ${options_type.section_reporting_type.show_reference_repeats}
        #end if
        
        ##population model
        #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set":
            --theta "${options_type.section_population_model_type.theta}"
            --ploidy "${options_type.section_population_model_type.ploidy}"
            ${options_type.section_population_model_type.pooled}
        #end if
        
        ##reference allele
        #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele":
            --use-reference-allele
            ${options_type.use_reference_allele_type.diploid_reference}
            --reference-quality "${options_type.use_reference_allele_type.reference_quality_mq},${options_type.use_reference_allele_type.reference_quality_bq}"
        #end if
        
        ##allele scope
        #if str( $options_type.section_allele_scope_type.section_allele_scope_type_selector ) == "set":
            ${options_type.section_allele_scope_type.no_snps}
            ${options_type.section_allele_scope_type.no_indels}
            ${options_type.section_allele_scope_type.no_mnps}
            ${options_type.section_allele_scope_type.no_complex}
            --use-best-n-alleles "${options_type.section_allele_scope_type.use_best_n_alleles}"
            #if $options_type.section_allele_scope_type.max_complex_gap:
                --max-complex-gap "${options_type.section_allele_scope_type.max_complex_gap}"
            #end if
        #end if
        
        ##indel realignment
        ${options_type.left_align_indels}
        
        ##input filters
        #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set":
            ${options_type.section_input_filters_type.use_duplicate_reads}
            #if str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "apply_filters":
                --min-mapping-quality "${options_type.section_input_filters_type.quality_filter_type.min_mapping_quality}"
                --min-base-quality "${options_type.section_input_filters_type.quality_filter_type.min_base_quality}"
                --min-supporting-quality "${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_bq}"
            #elif str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "standard_filters":
                --standard-filters
            #end if
            --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}"
            #if $options_type.section_input_filters_type.read_mismatch_limit:
                --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}"
            #end if
            --read-max-mismatch-fraction "${options_type.section_input_filters_type.read_max_mismatch_fraction}"
            #if $options_type.section_input_filters_type.read_snp_limit:
                --read-snp-limit "${options_type.section_input_filters_type.read_snp_limit}"
            #end if
            #if $options_type.section_input_filters_type.read_indel_limit:
                --read-indel-limit "${options_type.section_input_filters_type.read_indel_limit}"
            #end if
            --indel-exclusion-window "${options_type.section_input_filters_type.indel_exclusion_window}"
            --min-alternate-fraction "${options_type.section_input_filters_type.min_alternate_fraction}"
            --min-alternate-count "${options_type.section_input_filters_type.min_alternate_count}"
            --min-alternate-qsum "${options_type.section_input_filters_type.min_alternate_qsum}"
            --min-alternate-total "${options_type.section_input_filters_type.min_alternate_total}"
            --min-coverage "${options_type.section_input_filters_type.min_coverage}"
        #end if
        
        ##bayesian priors
        #if str( $options_type.section_bayesian_priors_type.section_bayesian_priors_type_selector ) == "set":
            ${options_type.section_bayesian_priors_type.no_ewens_priors}
            ${options_type.section_bayesian_priors_type.no_population_priors}
            ${options_type.section_bayesian_priors_type.hwe_priors}
        #end if
        
        ##observation prior expectations
        #if str( $options_type.section_observation_prior_expectations_type.section_observation_prior_expectations_type_selector ) == "set":
            ${options_type.section_observation_prior_expectations_type.binomial_obs_priors}
            ${options_type.section_observation_prior_expectations_type.allele_balance_priors}
        #end if
        
        ##algorithmic features
        #if str( $options_type.section_algorithmic_features_type.section_algorithmic_features_type_selector ) == "set":
            --site-selection-max-iterations "${options_type.section_algorithmic_features_type.site_selection_max_iterations}"
            --genotyping-max-iterations "${options_type.section_algorithmic_features_type.genotyping_max_iterations}"
            --genotyping-max-banddepth "${options_type.section_algorithmic_features_type.genotyping_max_banddepth}"
            --posterior-integration-limits "${options_type.section_algorithmic_features_type.posterior_integration_limits_n},${options_type.section_algorithmic_features_type.posterior_integration_limits_m}"
            ${options_type.section_algorithmic_features_type.no_permute}
            ${options_type.section_algorithmic_features_type.exclude_unobserved_genotypes}
            #if $options_type.section_algorithmic_features_type.genotype_variant_threshold:
                --genotype-variant-threshold "${options_type.section_algorithmic_features_type.genotype_variant_threshold}"
            #end if
            ${options_type.section_algorithmic_features_type.use_mapping_quality}
            --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}"
            ${options_type.section_algorithmic_features_type.no_marginals}
        #end if
    #end if
  </command>
  <inputs>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <repeat name="input_bams" title="Sample BAM file" min="1">
            <param name="input_bam" type="data" format="bam" label="BAM file">
              <validator type="unspecified_build" />
              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
            </param>
        </repeat>
        <param name="ref_file" type="select" label="Using reference genome">
          <options from_data_table="sam_fa_indexes">
            <!-- <filter type="sam_fa_indexes" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history"> <!-- FIX ME!!!! -->
        <repeat name="input_bams" title="Sample BAM file" min="1">
            <param name="input_bam" type="data" format="bam" label="BAM file" />
        </repeat>
        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
      </when>
    </conditional>
    
    <conditional name="options_type">
      <param name="options_type_selector" type="select" label="Basic or Advanced options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
        <!-- Do nothing here -->
      </when>
      <when value="advanced">
        
        <!-- output -->
        <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" />
        <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" />
        
        
        <!-- input -->
        <conditional name="target_limit_type">
          <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets">
            <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." />
          </when>
          <when value="limit_by_region">
            <param name="region_chromosome" type="text" label="Region Chromosome" value="" /> <!--only once? -->
            <param name="region_start" type="integer" label="Region Start" value="" />
            <param name="region_end" type="integer" label="Region End" value="" />
          </when>
        </conditional>
        <param name="input_sample_file" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" />
        <param name="input_populations_file" type="data" format="txt" label="Populations File" optional="True" />
        <param name="input_cnv_map_bed" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" />
        <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" label="Use variants reported in VCF file as input to the algorithm" />
            <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" />
        
        <!-- reporting -->
        <conditional name="section_reporting_type">
          <param name="section_reporting_type_selector" type="select" label="Set Reporting options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="pvar" type="float" label="Report sites if the probability that there is a polymorphism at the site is greater" value="0.0001" />
            <param name="show_reference_repeats" type="boolean" truevalue="--show-reference-repeats" falsevalue="" checked="False" label="Calculate and show information about reference repeats" />
          </when>
        </conditional>
        
        
        <!-- population model -->
        <conditional name="section_population_model_type">
          <param name="section_population_model_type_selector" type="select" label="Set population model options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="theta" type="float" label="expected mutation rate or pairwise nucleotide diversity among the population" value="0.001" help="This serves as the single parameter to the Ewens Sampling Formula prior model"/>
            <param name="ploidy" type="integer" label="default ploidy for the analysis" value="2" />
            <param name="pooled" type="boolean" truevalue="--pooled" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing" help="When using this flag, set --ploidy to the number of alleles in each sample." />
          </when>
        </conditional>
        
        <!-- reference allele -->
            <conditional name="use_reference_allele_type">
              <param name="use_reference_allele_type_selector" type="select" label="Include the reference allele in the analysis">
                <option value="do_not_include_reference_allele" selected="True">Do not include</option>
                <option value="include_reference_allele">Include</option>
              </param>
              <when value="do_not_include_reference_allele">
                <!-- Do nothing here -->
              </when>
              <when value="include_reference_allele">
                <param name="diploid_reference" type="boolean" truevalue="--diploid-reference" falsevalue="" checked="False" label="Treat reference as diploid" />
                <param name="reference_quality_mq" type="integer" label="Assign mapping quality" value="100" />
                <param name="reference_quality_bq" type="integer" label="Assign base quality" value="60" />
              </when>
            </conditional>     
        
        <!-- allele scope -->
        <conditional name="section_allele_scope_type">
          <param name="section_allele_scope_type_selector" type="select" label="Set allele scope options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="no_snps" type="boolean" truevalue="--no-snps" falsevalue="" checked="False" label="Ignore SNP alleles" />
            <param name="no_indels" type="boolean" truevalue="--no-indels" falsevalue="" checked="False" label="Ignore insertion and deletion alleles" />
            <param name="no_mnps" type="boolean" truevalue="--no-mnps" falsevalue="" checked="False" label="Ignore multi-nuceotide polymorphisms, MNPs" />
            <param name="no_complex" type="boolean" truevalue="--no-complex" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)" />
            <param name="use_best_n_alleles" type="integer" label="Evaluate only the best N SNP alleles" value="0" min="0" help="Ranked by sum of supporting quality scores; Set to 0 to use all" />
            <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/>
          </when>
        </conditional>
        
        <!-- indel realignment -->
        <!-- in FreeBayes < 0.9.9 the default is to not left-align indels and the available option is - -left-align-indels,
             in FreeBayes >= 0.9.9 the default is to left-align indels and the available option is - -dont-left-align-indels -->
        <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left align indels" />
        
        <!-- input filters -->
        <conditional name="section_input_filters_type">
          <param name="section_input_filters_type_selector" type="select" label="Set input filters options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <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" />
            <conditional name="quality_filter_type">
              <param name="quality_filter_type_selector" type="select" label="Apply Quality filters">
                <option value="standard_filters" selected="True">Apply standard</option>
                <option value="apply_filters">Apply specified</option>
              </param>
              <when value="standard_filters">
                <!-- Do nothing here --> <!-- standard-filters -->
              </when>
              <when value="apply_filters">
                <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="0" />
                <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="0" />
                <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" />
                <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" />
              </when>
            </conditional>
            <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is &gt;=" value="10" />
            <param name="read_mismatch_limit" type="integer" label="Exclude reads with more than N mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold" value="" optional="True" />
            <param name="read_max_mismatch_fraction" type="float" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold" value="1.0" />
            <param name="read_snp_limit" type="integer" label="Exclude reads with more than N base mismatches, ignoring gaps with quality &gt;= mismatch-base-quality-threshold" value="" optional="True" />
            <param name="read_indel_limit" type="integer" label="Exclude reads with more than N separate gaps" value="" optional="True" />
            <param name="indel_exclusion_window" type="integer" label="Ignore portions of alignments this many bases from a putative insertion or deletion allele" value="0" />
            <param name="min_alternate_fraction" type="float" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" value="0" />
            <param name="min_alternate_count" type="integer" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" value="1" />
            <param name="min_alternate_qsum" type="integer" label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" value="0" />
            <param name="min_alternate_total" type="integer" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" value="1" />
            <param name="min_coverage" type="integer" label="Require at least this coverage to process a site" value="0" />
          </when>
        </conditional>
        
        
        <!-- bayesian priors -->
        <conditional name="section_bayesian_priors_type">
          <param name="section_bayesian_priors_type_selector" type="select" label="Set bayesian priors options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="no_ewens_priors" type="boolean" truevalue="--no-ewens-priors" falsevalue="" checked="False" label="Turns off the Ewens' Sampling Formula component of the priors" />
            <param name="no_population_priors" type="boolean" truevalue="--no-population-priors" falsevalue="" checked="False" label="No population priors" help="Equivalent to --pooled --no-ewens-priors" />
            <param name="hwe_priors" type="boolean" truevalue="--hwe-priors" falsevalue="" checked="False" label="Use the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
          </when>
        </conditional>
        
        <!-- observation prior expectations -->
        <conditional name="section_observation_prior_expectations_type">
          <param name="section_observation_prior_expectations_type_selector" type="select" label="Set observation prior expectations options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="binomial_obs_priors" type="boolean" truevalue="--binomial-obs-priors" falsevalue="" checked="False" label="Incorporate expectations about osbervations into the priors, Uses read placement probability, strand balance probability, and read position (5'-3') probability" />
            <param name="allele_balance_priors" type="boolean" truevalue="--allele-balance-priors" falsevalue="" checked="False" label="Use aggregate probability of observation balance between alleles as a component of the priors.  Best for observations with minimal inherent reference bias" />
          </when>
        </conditional>
        
        
        <!-- algorithmic features -->
        <conditional name="section_algorithmic_features_type">
          <param name="section_algorithmic_features_type_selector" type="select" label="Set algorithmic features options">
            <option value="do_not_set" selected="True">Do not set</option>
            <option value="set">Set</option>
          </param>
          <when value="do_not_set">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="site_selection_max_iterations" type="integer" label="Uses hill-climbing algorithm to search posterior space for N iterations to determine if the site should be evaluated." value="5" help="Set to 0 to prevent use of this algorithm for site selection, and to a low integer for improvide site selection at a slight performance penalty" />
            <param name="genotyping_max_iterations" type="integer" label="Iterate no more than N times during genotyping step" value="25" />
            <param name="genotyping_max_banddepth" type="integer" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" value="6" />
            <param name="posterior_integration_limits_n" type="integer" label="Posteriror integration limit N" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="1" />
            <param name="posterior_integration_limits_m" type="integer" label="Posteriror integration limit M" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="3" />
            <param name="no_permute" type="boolean" truevalue="--no-permute" falsevalue="" checked="False" label="Do not scale prior probability of genotype combination given allele frequency by the number of permutations of included genotypes" />
            <param name="exclude_unobserved_genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" />
            <param name="genotype_variant_threshold" 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" value="" optional="True" />
            <param name="use_mapping_quality" type="boolean" truevalue="--use-mapping-quality" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods" />
            <param name="read_dependence_factor" type="float" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" value="0.9" />
            <param name="no_marginals" type="boolean" truevalue="--no-marginals" falsevalue="" checked="False" label="Do not calculate the marginal probability of genotypes.  Saves time and improves scaling performance in large populations" />
          </when>
        </conditional>
        
        
      </when>
    </conditional>
    
  </inputs>
  <outputs>
    <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
    <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
        <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter>
    </data>
    <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
        <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter>
    </data>
  </outputs>
  <tests>
    <test>
     <param name="reference_source_selector" value="history" />
      <param name="ref_file" ftype="fasta" value="phiX.fasta"/>
      <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/>
      <param name="options_type_selector" value="basic"/>
      <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
    </test>
  </tests>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <help>
**What it does**

This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file.

FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.

In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. 

Go `here &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_ for details on FreeBayes.

------

**Inputs**

FreeBayes accepts an input aligned BAM file.


**Outputs**

The output is in the VCF format.

-------

**Settings**::

  input and output:

   -b --bam FILE   Add FILE to the set of BAM files to be analyzed.
   -c --stdin      Read BAM input on stdin.
   -v --vcf FILE   Output VCF-format results to FILE.
   -f --fasta-reference FILE
                   Use FILE as the reference sequence for analysis.
                   An index file (FILE.fai) will be created if none exists.
                   If neither --targets nor --region are specified, FreeBayes
                   will analyze every position in this reference.
   -t --targets FILE
                   Limit analysis to targets listed in the BED-format FILE.
   -r --region &lt;chrom&gt;:&lt;start_position&gt;..&lt;end_position&gt;
                   Limit analysis to the specified region, 0-base coordinates,
                   end_position not included (same as BED format).
   -s --samples FILE
                   Limit analysis to samples listed (one per line) in the FILE.
                   By default FreeBayes will analyze all samples in its input
                   BAM files.
   --populations FILE
                   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.
   -A --cnv-map FILE
                   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.
   -L --trace FILE  Output an algorithmic trace to FILE.
   --failed-alleles FILE
                   Write a BED file of the analyzed positions which do not
                   pass --pvar to FILE.
   -@ --variant-input VCF
                   Use variants reported in VCF file as input to the algorithm.
                   A report will be generated for every record in the VCF file.
   -l --only-use-input-alleles
                   Only provide variant calls and genotype likelihoods for sites
                   and alleles which are provided in the VCF input, and provide
                   output in the VCF for all input alleles, not just those which
                   have support in the data.
   --haplotype-basis-alleles VCF
                   When specified, only variant alleles provided in this input
                   VCF will be used for the construction of complex or haplotype
                   alleles.

  reporting:

   -P --pvar N     Report sites if the probability that there is a polymorphism
                   at the site is greater than N.  default: 0.0001
   -_ --show-reference-repeats
                   Calculate and show information about reference repeats in
                   the VCF output.

  population model:

   -T --theta N    The expected mutation rate or pairwise nucleotide diversity
                   among the population under analysis.  This serves as the
                   single parameter to the Ewens Sampling Formula prior model
                   default: 0.001
   -p --ploidy N   Sets the default ploidy for the analysis to N.  default: 2
   -J --pooled     Assume that samples result from pooled sequencing.
                   When using this flag, set --ploidy to the number of
                   alleles in each sample.

  reference allele:

   -Z --use-reference-allele
                   This flag includes the reference allele in the analysis as
                   if it is another sample from the same population.
   -H --diploid-reference
                   If using the reference sequence as a sample (-Z),
                   treat it as diploid.  default: false (reference is haploid)
   --reference-quality MQ,BQ
                   Assign mapping quality of MQ to the reference allele at each
                   site and base quality of BQ.  default: 100,60

  allele scope:

   -I --no-snps    Ignore SNP alleles.
   -i --no-indels  Ignore insertion and deletion alleles.
   -X --no-mnps    Ignore multi-nuceotide polymorphisms, MNPs.
   -u --no-complex Ignore complex events (composites of other classes).
   -n --use-best-n-alleles N
                   Evaluate only the best N SNP alleles, ranked by sum of
                   supporting quality scores.  (Set to 0 to use all; default: all)
   -E --max-complex-gap N
                   Allow complex alleles with contiguous embedded matches of up
                   to this length.

  indel realignment:

   -O --left-align-indels
                   Left-realign and merge gaps embedded in reads. default: false

  input filters:

   -4 --use-duplicate-reads
                   Include duplicate-marked alignments in the analysis.
                   default: exclude duplicates
   -m --min-mapping-quality Q
                   Exclude alignments from analysis if they have a mapping
                   quality less than Q.  default: 30
   -q --min-base-quality Q
                   Exclude alleles from analysis if their supporting base
                   quality is less than Q.  default: 20
   -R --min-supporting-quality MQ,BQ
                   In order to consider an alternate allele, at least one supporting
                   alignment must have mapping quality MQ, and one supporting 
                   allele must have base quality BQ. default: 0,0, unset
   -Q --mismatch-base-quality-threshold Q
                   Count mismatches toward --read-mismatch-limit if the base
                   quality of the mismatch is &gt;= Q.  default: 10
   -U --read-mismatch-limit N
                   Exclude reads with more than N mismatches where each mismatch
                   has base quality &gt;= mismatch-base-quality-threshold.
                   default: ~unbounded
   -z --read-max-mismatch-fraction N
                   Exclude reads with more than N [0,1] fraction of mismatches where
                   each mismatch has base quality &gt;= mismatch-base-quality-threshold
                   default: 1.0
   -$ --read-snp-limit N
                   Exclude reads with more than N base mismatches, ignoring gaps
                   with quality &gt;= mismatch-base-quality-threshold.
                   default: ~unbounded
   -e --read-indel-limit N
                   Exclude reads with more than N separate gaps.
                   default: ~unbounded
   -0 --standard-filters  Use stringent input base and mapping quality filters
                   Equivalent to -m 30 -q 20 -R 0 -S 0
   -x --indel-exclusion-window
                   Ignore portions of alignments this many bases from a
                   putative insertion or deletion allele.  default: 0
   -F --min-alternate-fraction N
                   Require at least this fraction of observations supporting
                   an alternate allele within a single individual in the
                   in order to evaluate the position.  default: 0.0
   -C --min-alternate-count N
                   Require at least this count of observations supporting
                   an alternate allele within a single individual in order
                   to evaluate the position.  default: 1
   -3 --min-alternate-qsum N
                   Require at least this sum of quality of observations supporting
                   an alternate allele within a single individual in order
                   to evaluate the position.  default: 0
   -G --min-alternate-total N
                   Require at least this count of observations supporting
                   an alternate allele within the total population in order
                   to use the allele in analysis.  default: 1
   -! --min-coverage N
                   Require at least this coverage to process a site.  default: 0

  bayesian priors:

   -Y --no-ewens-priors
                   Turns off the Ewens' Sampling Formula component of the priors.
   -k --no-population-priors
                   Equivalent to --pooled --no-ewens-priors
   -w --hwe-priors Use the probability of the combination arising under HWE given
                   the allele frequency as estimated by observation frequency.

  observation prior expectations:

   -V --binomial-obs-priors
                   Incorporate expectations about osbervations into the priors,
                   Uses read placement probability, strand balance probability,
                   and read position (5'-3') probability.
   -a --allele-balance-priors
                   Use aggregate probability of observation balance between alleles
                   as a component of the priors.  Best for observations with minimal
                   inherent reference bias.

  algorithmic features:

   -M --site-selection-max-iterations N
                   Uses hill-climbing algorithm to search posterior space for N
                   iterations to determine if the site should be evaluated.  Set to 0
                   to prevent use of this algorithm for site selection, and
                   to a low integer for improvide site selection at a slight
                   performance penalty. default: 5.
   -B --genotyping-max-iterations N
                   Iterate no more than N times during genotyping step. default: 25.
   --genotyping-max-banddepth N
                   Integrate no deeper than the Nth best genotype by likelihood when
                   genotyping. default: 6.
   -W --posterior-integration-limits N,M
                   Integrate all genotype combinations in our posterior space
                   which include no more than N samples with their Mth best
                   data likelihood. default: 1,3.
   -K --no-permute
                   Do not scale prior probability of genotype combination given allele
                   frequency by the number of permutations of included genotypes.
   -N --exclude-unobserved-genotypes
                   Skip sample genotypings for which the sample has no supporting reads.
   -S --genotype-variant-threshold N
                   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.  default: ~unbounded
   -j --use-mapping-quality
                   Use mapping quality of alleles when calculating data likelihoods.
   -D --read-dependence-factor N
                   Incorporate non-independence of reads by scaling successive
                   observations by this factor during data likelihood
                   calculations.  default: 0.9
   -= --no-marginals
                   Do not calculate the marginal probability of genotypes.  Saves
                   time and improves scaling performance in large populations.


------

**Citation**

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

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

  </help>
</tool>