Mercurial > repos > computational-metabolomics > mspurity_createdatabase
comparison purityX.R @ 10:f5043704dd62 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5
author | computational-metabolomics |
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date | Fri, 13 Sep 2024 12:27:15 +0000 |
parents | 751b7378a683 |
children |
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9:751b7378a683 | 10:f5043704dd62 |
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14 make_option("--isotope_matrix", type = "character"), | 14 make_option("--isotope_matrix", type = "character"), |
15 make_option("--purityType", default = "purityFWHMmedian"), | 15 make_option("--purityType", default = "purityFWHMmedian"), |
16 make_option("--singleFile", default = 0), | 16 make_option("--singleFile", default = 0), |
17 make_option("--cores", default = 4), | 17 make_option("--cores", default = 4), |
18 make_option("--xgroups", type = "character"), | 18 make_option("--xgroups", type = "character"), |
19 make_option("--rdata_name", default = "xset"), | |
20 make_option("--camera_xcms", default = "xset"), | 19 make_option("--camera_xcms", default = "xset"), |
21 make_option("--files", type = "character"), | 20 make_option("--files", type = "character"), |
22 make_option("--galaxy_files", type = "character"), | 21 make_option("--galaxy_files", type = "character"), |
23 make_option("--choose_class", type = "character"), | 22 make_option("--choose_class", type = "character"), |
24 make_option("--ignore_files", type = "character"), | 23 make_option("--ignore_files", type = "character"), |
61 rtraw_columns <- FALSE | 60 rtraw_columns <- FALSE |
62 } else { | 61 } else { |
63 rtraw_columns <- TRUE | 62 rtraw_columns <- TRUE |
64 } | 63 } |
65 | 64 |
66 loadRData <- function(rdata_path, xset_name) { | 65 loadRData <- function(rdata_path, xnames) { |
67 # loads an RData file, and returns the named xset object if it is there | 66 # loads an RData file, and returns the named xset object if it is there |
68 load(rdata_path) | 67 load(rdata_path) |
69 return(get(ls()[ls() == xset_name])) | 68 return(get(ls()[ls() %in% xnames])) |
70 } | 69 } |
71 | 70 |
72 | 71 |
73 | 72 |
74 | 73 |
88 } | 87 } |
89 return(xset) | 88 return(xset) |
90 } | 89 } |
91 } | 90 } |
92 | 91 |
93 target_obj <- loadRData(opt$xset_path, opt$rdata_name) | 92 target_obj <- loadRData(opt$xset_path, c('xset', 'xa', 'xdata')) |
94 | 93 |
95 if (opt$camera_xcms == "camera") { | 94 if (opt$camera_xcms == "camera") { |
96 xset <- target_obj@xcmsSet | 95 xset <- target_obj@xcmsSet |
97 } else { | 96 } else { |
98 xset <- target_obj | 97 xset <- target_obj |