view snpSift_vcfCheck.xml @ 11:b884686a80dc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a

<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0">
    <description>basic checks for Vcf specification compliance</description>
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <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>
    <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>