<tool id="snpsift_vartype" name="SnpSift Variant Type" version="3.6">
    <description>Annotate with variant type</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
        java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2&gt; $log &gt; $output
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
    </inputs>
    <outputs>
        <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
        <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
    </outputs>
    <expand macro="stdio" />
    <tests>
    </tests>
    <help>
**What it does**

This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense).

.. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType

------

**License and citation**

This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

If you use this tool in Galaxy, please cite |Cuccuru2014|_.

.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, doi:10.1093/bioinformatics/btu135
.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135

@CITATION_SECTION@
    </help>
</tool>

Add wrapper for SnpSift varType.
Add wrapper for SnpSift varType.
