view extract_variants.xml @ 0:bf8841b0a6b0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7

<tool id="gvcftools_extract_variants" name="Extract Variants from gVCF files" version="0.1">
  <description>Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.</description>

  <requirements>
      <requirement type="package" version="0.17.0">gvcftools</requirement>
  </requirements>

  <command detect_errors="aggressive">
  <![CDATA[
      extract_variants
        #if str( $advanced.advanced_options_selector ) == 'true':
         '${advanced.skip_header}' '${advanced.invert}'
        #end if
      < '${gvcf_input}' > '${vcf_output}'
  ]]>]
  </command>

  <inputs>
    <param name="gvcf_input" type="data" format="vcf" label="Variants (gVCF format)" />
    <conditional name="advanced">
      <param name="advanced_options_selector" type="select" label="Advanced options">
        <option value="true">Show advanced options</option>
        <option value="false" selected="True">Don't show advanced options</option>
      </param>
      <when value="true">
        <param type="boolean" name="skip_header" argument="--skip-header"
          truevalue="--skip-header" falsevalue=""
          label="Write the variants output file without a header" />
        <param type="boolean" argument="--invert"
          truevalue="--invert" falsevalue=""
          label="Invert the filter so that only non-variant records are output" />
      </when>
      <when value="false"></when>
    </conditional>
  </inputs>

  <outputs>
    <data name="vcf_output" format="vcf" />
  </outputs>

  <tests>
    <test>
      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
      <output name="vcf_output" ftype="vcf" value="variants_output1.vcf" />
    </test>
    <test>
      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
      <param name="advanced_options_selector" value="true" />
      <param name="skip_header" value="True" />
      <output name="vcf_output" ftype="vcf" value="variants_noheader_output1.vcf" />
    </test>
    <test>
      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
      <param name="advanced_options_selector" value="true" />
      <param name="invert" value="True" />
      <output name="vcf_output" ftype="vcf" value="nonvariants_output1.vcf" />
    </test>

  </tests>

  <help>
    <![CDATA[
    Extract variants from a gVCF field, removing all non-variant blocks to yield a smaller variant only VCF file.

    From the `gvcftools`_ toolkit.

    .. _gvcftools: https://sites.google.com/site/gvcftools/
    ]]>
  </help>
  <citations>
        <citation type="bibtex">
           @unpublished{gvcftools,
              author = {Illumina, Inc.},
              title  = {gvcftools},
              url    = {https://sites.google.com/site/gvcftools/}
            }
        </citation>
  </citations>
</tool>