view snpSift_vcfCheck.xml @ 9:88f4997ccb02 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

<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[
      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><![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>