view snpEff_databases.xml @ 17:13d81e5226cd

Put gene info in Summary Report extra_files_path

<tool id="snpEff_databases" name="SnpEff Available Databases" version="4.0.0">
    <description></description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
    java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > $snpeff_dbs 
    </command>
    <inputs>
    </inputs>
    <outputs>
        <data format="tabular" name="snpeff_dbs" label="${tool.name} available databases" />
    </outputs>
    <expand macro="stdio" />
    <help>

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

    </help>
</tool>