comparison freebayes.xml @ 5:949ac66308a7

Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.

4:e54bb199a47b

<?xml version="1.0"?>
<tool id="freebayes" name="FreeBayes" version="0.0.2">
  <requirements>
    <requirement type="package" version="0.9.4_a46483351fd0196637614121868fb5c386612b55">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"

        #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
        
        ##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}

        ${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( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters":
                --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}"
                --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}"
                --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}"
            #else:
                --no-filters
            #end if
            --mismatch-base-quality-threshold "${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

          <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>
        
        
        <!-- 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>

          <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="no_filter_type">
              <param name="no_filter_type_selector" type="select" label="Apply filters">
                <option value="apply_filters" selected="True">Apply</option>
                <option value="no_filters">Do not apply</option>
              </param>
              <when value="no_filters">
                <!-- Do nothing here --> <!-- no-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="30" />
                <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" />
                <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="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"/>
      <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" />
      <output name="output_trace" file="freebayes_out_1.output_trace" /> -->
    </test>
  </tests>
  <help>
**What it does**

   -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.

  reporting:

   -P --pvar N     Report sites if the probability that there is a polymorphism
                   at the site is greater than N.  default: 0.0001

                   with quality >= mismatch-base-quality-threshold.
                   default: ~unbounded
   -e --read-indel-limit N
                   Exclude reads with more than N separate gaps.
                   default: ~unbounded
   -0 --no-filters Do not use any input base and mapping quality filters
                   Equivalent to -m 0 -q 0 -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

------

**Citation**

For the underlying tool, please cite `FreeBayes <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_.

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

  </help>
</tool>

5:949ac66308a7

<?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">samtools</requirement>
  </requirements>
  <description> - Bayesian genetic variant detector</description>
  <command>
    ##set up input files
    #set $reference_fasta_filename = "localref.fa"

        #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}

        ${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

          <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>

          <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="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>
  <help>
**What it does**

   -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

                   with quality >= 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

------

**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>`_.

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

  </help>
</tool>