Mercurial > repos > devteam > table_annovar

comparison table_annovar.xml @ 6:091154194ce8 draft

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author devteam
date Wed, 12 Feb 2014 16:32:16 -0500
parents 7d2a81d29ca4
children 08b003ee9db7
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5:7d2a81d29ca4 6:091154194ce8
38 38
39 ## Reduce variants. 39 ## Reduce variants.
40 ; 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 40 ; table_annovar.pl input.avinput ${__get_data_table_entry__('annovar_indexes', 'dbkey', $input.dbkey, 'path')} -protocol ${protocol} -operation ${operation} -nastring NA -buildver ${input.dbkey} --outfile output
41 41
42 ## Process annotated table to remove "NA" strings from numerical columns and copy to output. 42 ## Process annotated table to remove "NA" strings from numerical columns and copy to output.
43 ; cat output.${input.dbkey}_multianno.txt | \$SCRIPT_PATH/replace_NA.py > ${output} 43 ; cat output.${input.dbkey}_multianno.txt | python \$SCRIPT_PATH/replace_NA.py > ${output}
44 </command> 44 </command>
45 45
46 <inputs> 46 <inputs>
47 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help=""> 47 <param name="input" type="data" format="vcf" metadata_name="dbkey" label="Variants" help="">
48 <validator type="unspecified_build" /> 48 <validator type="unspecified_build" />