view snpEff_macros.xml @ 3:1739678def32

Add vcfCheck and test cases

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.0">snpEff</requirement>
        </requirements>
    </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
  </xml>
  <token name="@EXTERNAL_DOCUMENTATION@">

For details about this tool, please go to:
	http://snpeff.sourceforge.net/SnpEff_manual.html

  </token>
  <token name="@CITATION_SECTION@">------

**Citation**

For the underlying tool, please cite the following two publications:

SnpEff citation:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

SnpSift citation:
"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.

  </token>
</macros>