view snpSift_vcfCheck.xml @ 8:5fab4f81391d draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"

<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.galaxy0">
    <description>basic checks for VCF specification compliance</description>
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
SnpSift -Xmx2G vcfCheck
'$input'
> '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="vcf" label="Variant input file in VCF format to check"/>
    </inputs>
    <outputs>
        <data name="output" format="vcf" />
    </outputs>
    <tests>
        <test expect_exit_code="0">
            <param name="input" ftype="vcf" value="test_bad.vcf"/>
            <assert_stderr>
                <has_text text="Errors" />
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
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
    ]]></help>
    <expand macro="citations" />
</tool>