comparison data_manager/customProDB_annotation.R @ 7:7399b23db662 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 08 Jun 2016 15:53:39 -0400
parents c922df2f9c2a
children f4badf0bf23a
comparison
equal deleted inserted replaced
6:c922df2f9c2a 7:7399b23db662
47 } 47 }
48 else 48 else
49 { 49 {
50 dbsnp = NULL 50 dbsnp = NULL
51 } 51 }
52 52
53 if (length(cosmic) > 0 && cosmic && grepl("^hg", dbkey)) 53 use_cosmic = NULL
54 if (length(cosmic) > 0)
54 { 55 {
55 use_cosmic = TRUE 56 if (grepl("^hg", dbkey))
56 } 57 {
57 else 58 use_cosmic = TRUE
58 { 59 }
59 use_cosmic = NULL 60 else
61 {
62 gstop("COSMIC annotation requested but dbkey does not indicate a human genome (e.g. hg19)")
63 }
60 } 64 }
61 65
62 suppressPackageStartupMessages(library(rjson)) 66 suppressPackageStartupMessages(library(rjson))
63 params = fromJSON(file=outputFile) 67 params = fromJSON(file=outputFile)
64 target_directory = params$output_data[[1]]$extra_files_path 68 target_directory = params$output_data[[1]]$extra_files_path