comparison table_annovar.xml @ 6:091154194ce8 draft

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5:7d2a81d29ca4

        ## Reduce variants.
        ; table_annovar.pl input.avinput ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring NA -buildver ${input.dbkey} --outfile output

        ## Process annotated table to remove "NA" strings from numerical columns and copy to output.
        ; cat output.${input.dbkey}_multianno.txt | \$SCRIPT_PATH/replace_NA.py > ${output}
    </command>

    <inputs>
        <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
        <validator type="unspecified_build" />

6:091154194ce8

        ## Reduce variants.
        ; table_annovar.pl input.avinput ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring NA -buildver ${input.dbkey} --outfile output

        ## Process annotated table to remove "NA" strings from numerical columns and copy to output.
        ; cat output.${input.dbkey}_multianno.txt | python \$SCRIPT_PATH/replace_NA.py > ${output}
    </command>

    <inputs>
        <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
        <validator type="unspecified_build" />