view snpSift_vcfCheck.xml @ 3:1739678def32

Add vcfCheck and test cases

<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0">
    <description>basic checks for Vcf specification compliance</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/>
    </inputs>
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <expand macro="stdio" />
    <tests>
        <test>
            <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Errors" />
		</assert_contents>
            </output>
        </test>
    </tests>
    <help>

Perform some basic check ups on VCF files to spot common problems.

SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. 

@EXTERNAL_DOCUMENTATION@
	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck

@CITATION_SECTION@

    </help>
</tool>