comparison table_annovar.xml @ 2:9c75a9b5ecd2

Add help to tool.

1:a6c64723f5ce

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

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

        #set operation = ','.join( $operation ) 

        ## 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

        ## Copy annotated table to output.
        ; cp output.${input.dbkey}_multianno.txt ${output}
    </command>

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

    <tests>
    </tests>

    <help>
    </help>
</tool>

2:9c75a9b5ecd2

<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>

        #set operation = ','.join( $operation ) 

        ## 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" />

    <tests>
    </tests>

    <help>
**What it does**

This tool will annotate variants using specified gene annotations, regions, and filtering databases. Input is a VCF dataset, and output is a table of annotations for each variant in the 
VCF dataset.

**ANNOVAR Website and Documentation**

Website: http://www.openbioinformatics.org/annovar/

Paper: http://nar.oxfordjournals.org/content/38/16/e164

**Important Usage Note**

ANNOVAR is open-source and free for non-profit use. If you use it for commercial purposes, please contact BIOBASE ([e-mail]) directly for license related issues. Also see http://www.openbioinformatics.org/annovar/annovar_faq.html#license

    </help>
</tool>