view snpSift_vcfCheck.xml @ 7:2e497a770bca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"

<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>