comparison snpSift_int.xml @ 8:2f40467536cf draft

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

7:c29f29a6f26c

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>

You can filter using intervals (BED file).

@EXTERNAL_DOCUMENTATION@
    http://snpeff.sourceforge.net/SnpSift.html#intervals

@CITATION_SECTION@

]]>
    </help>
</tool>

8:2f40467536cf

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>

You can filter using intervals (BED file).

@EXTERNAL_DOCUMENTATION@
    http://snpeff.sourceforge.net/SnpSift.html#intervals

]]>
    </help>
    <expand macro="citations" />
</tool>