Mercurial > repos > devteam > table_annovar
changeset 2:9c75a9b5ecd2
Add help to tool.
| author | jeremy goecks <jeremy.goecks@emory.edu> |
|---|---|
| date | Mon, 27 Jan 2014 11:32:02 -0500 |
| parents | a6c64723f5ce |
| children | 5cb2020a097a |
| files | table_annovar.xml |
| diffstat | 1 files changed, 18 insertions(+), 3 deletions(-) [+] |
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--- a/table_annovar.xml Mon Dec 02 15:31:17 2013 -0500 +++ b/table_annovar.xml Mon Jan 27 11:32:02 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="table_annovar" name="Annotate VCF" version="0.1"> +<tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.1"> <description>with functional information using ANNOVAR</description> <requirements> @@ -38,8 +38,8 @@ ## 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 ${output} + ## Process annotated table to remove "NA" strings from numerical columns and copy to output. + ; cat output.${input.dbkey}_multianno.txt | replace_NA.py > ${output} </command> <inputs> @@ -81,5 +81,20 @@ </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 (info@biobase-international.com) directly for license related issues. Also see http://www.openbioinformatics.org/annovar/annovar_faq.html#license + </help> </tool>