comparison table_annovar.xml @ 5:7d2a81d29ca4 draft

Uploaded

4:0f07aec558b9

<tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.1">
    <description>with functional information using ANNOVAR</description>

    <requirements>
        <requirement type="package">annovar</requirement>
    </requirements>

    <command>
        ## Convert VCF to AV input format.
        convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput

        ## 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 | replace_NA.py > ${output}
    </command>

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

5:7d2a81d29ca4

<tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.1">
    <description>with functional information using ANNOVAR</description>

    <requirements>
        <requirement type="package">annovar</requirement>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
    </requirements>

    <command>
        ## Convert VCF to AV input format.
        convert2annovar.pl -format vcf4 -includeinfo ${input} > input.avinput

        ## 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" />