view snpSift_vcfCheck.xml @ 2:bf8c1526871b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1">
    <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[
        @CONDA_SNPSIFT_JAR_PATH@ &&
        java -Xmx2G -jar "\$SNPSIFT_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_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>