comparison variant_annotator.xml @ 1:25b1bbfe9d13 draft

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit 4551dc00ae1447b86952c0c8e845496c264f3ccb

0:6e985e2e0802

      </when>
      <when value="choose">
        <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" 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="VariantAnnotator" column="tools_valid_for"/>
          </options>
        </param>
      </when>
    </conditional>

    <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
    <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &amp;lt;MendelViolationGenotypeQualityThreshold&amp;gt;"/>
    <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="VariantAnnotator" column="tools_valid_for"/>
      </options>
    </param>

  </inputs>
  <outputs>

1:25b1bbfe9d13

      </when>
      <when value="choose">
        <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" 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="3" separator=","/>
            <filter type="static_value" value="VariantAnnotator" column="3"/>
          </options>
        </param>
      </when>
    </conditional>

    <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
    <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &amp;lt;MendelViolationGenotypeQualityThreshold&amp;gt;"/>
    <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="3" separator=","/>
        <filter type="static_value" value="VariantAnnotator" column="3"/>
      </options>
    </param>

  </inputs>
  <outputs>