| Previous changeset 4:0f07aec558b9 (2014-02-12) Next changeset 6:091154194ce8 (2014-02-12) |
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Commit message:
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modified:
table_annovar.xml |
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| diff -r 0f07aec558b9 -r 7d2a81d29ca4 table_annovar.xml --- a/table_annovar.xml Wed Feb 12 16:05:46 2014 -0500 +++ b/table_annovar.xml Wed Feb 12 16:06:05 2014 -0500 |
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| @@ -3,6 +3,7 @@ <requirements> <requirement type="package">annovar</requirement> + <requirement type="set_environment">SCRIPT_PATH</requirement> </requirements> <command> @@ -39,7 +40,7 @@ ; 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 > ${output} + ; cat output.${input.dbkey}_multianno.txt | \$SCRIPT_PATH/replace_NA.py > ${output} </command> <inputs> |