Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
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 |
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date | Wed, 08 Jun 2016 15:53:39 -0400 |
parents | c922df2f9c2a |
children | f4badf0bf23a |
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6:c922df2f9c2a | 7:7399b23db662 |
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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 |