comparison haplotype_caller.xml @ 4:f244b8209eb8 draft

bug fix release

3:2553f84b8174

<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.7">
  <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>

        <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">
          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
          <options from_data_table="gatk2_annotations">
            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
          </options>
        </param>
        <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
          <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
        </repeat>

    <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
          <options from_data_table="gatk2_annotations">
            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
          </options>
        </param>

        <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp  comparison VCF file"/>
        <param name="contamination_fraction_to_filter" type="float" value="0.05" optional="true" label="contamination_fraction_to_filter" help="--contamination_fraction_to_filter / -contamination  Fraction of contamination in sequencing data (for all samples) to aggressively remove">

 genotypeFullActiveRegion    If specified, alternate alleles are considered to be the full active region for the purposes of genotyping
 max_alternate_alleles       Maximum number of alternate alleles to genotype

@CITATION_SECTION@
  </help>
</tool>

4:f244b8209eb8

<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.0">
  <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>

        <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">
          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
          <options from_data_table="gatk2_annotations">
            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
            <filter type="static_value" value="HaplotypeCaller" column="tools_valid_for"/>
          </options>
        </param>
        <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
          <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
        </repeat>

    <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
          <options from_data_table="gatk2_annotations">
            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
            <filter type="static_value" value="HaplotypeCaller" column="tools_valid_for"/>
          </options>
        </param>

        <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp  comparison VCF file"/>
        <param name="contamination_fraction_to_filter" type="float" value="0.05" optional="true" label="contamination_fraction_to_filter" help="--contamination_fraction_to_filter / -contamination  Fraction of contamination in sequencing data (for all samples) to aggressively remove">

 genotypeFullActiveRegion    If specified, alternate alleles are considered to be the full active region for the purposes of genotyping
 max_alternate_alleles       Maximum number of alternate alleles to genotype

@CITATION_SECTION@
  </help>
  <expand macro="citations" />
</tool>