view variant_effect_predictor/variant_effect_predictor.xml @ 0:21066c0abaf5 draft

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<tool id="variant_effect_predictor" name="Variant Effect Predictor" version="2.6">
  <description>Get consequences of variants</description>
  <command interpreter="perl">
    variant_effect_predictor.pl
      -format vcf -quiet -force -fork 4
      -cache -dir /mnt/galaxyIndices/vep/
      -i $input -o $output $output_format
      $check_existing $check_ref $regulatory
      $hgnc
      -terms $terms $sift $polyphen
  </command>
  <inputs>
    <param format="vcf" name="input" type="data" label="Input file"/>
    
    <param name="output_format" type="select" label="Output format">
      <option value="" selected="true">Default</option>
      <option value="-vcf">VCF</option>
      <option value="-gvf">GVF</option>
    </param>
    
    <param name="terms" type="select" label="Consequence types">
      <option value="so" selected="true">Sequence Ontology (SO)</option>
      <option value="ensembl">Ensembl</option>
    </param>
    
    <param name="sift" type="select" label="SIFT predictions">
      <option value="">None</option>
      <option value="-sift s">Score only</option>
      <option value="-sift p">Prediction only</option>
      <option value="-sift b" selected="true">Score and prediction</option>
    </param>
    
    <param name="polyphen" type="select" label="PolyPhen predictions">
      <option value="">None</option>
      <option value="-polyphen s">Score only</option>
      <option value="-polyphen p">Prediction only</option>
      <option value="-polyphen b" selected="true">Score and prediction</option>
    </param>
    
    
    <param name="check_existing" type="select" label="Check for existing co-located variations">
      <option value="">no</option>
      <option value="-check_existing" selected="true">yes</option>
    </param>
    
    <param name="check_ref" type="select" label="Sanity check supplied reference allele against Ensembl reference">
      <option value="" selected="true">no</option>
      <option value="-check_ref">yes</option>
    </param>
    
    <param name="regulatory" type="select" label="Get regulatory consequences">
      <option value="">no</option>
      <option value="-regulatory" selected="true">yes</option>
    </param>
    
    <param name="hgnc" type="select" label="Add HGNC identifiers for genes where available">
      <option value="" selected="true">no</option>
      <option value="-hgnc">yes</option>
    </param>
    
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <help>
This tool calculates consequences of variants using Ensembl annotations
  </help>

</tool>