view snpSift_vcfCheck.xml @ 4:b04635ebfab0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 9d2052269bfbca81a5f9cd10c3153e611358a329

<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0">
    <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>