Mercurial > repos > computational-metabolomics > mspurity_combineannotations

comparison createMSP.R @ 0:de93f6aac760 draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:21:39 +0000
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-1:000000000000 0:de93f6aac760
1 library(optparse)
2 library(msPurity)
3 print(sessionInfo())
4
5 # Get the parameter
6 option_list <- list(
7 make_option("--rdata_input", type = "character"),
8 make_option("--method", type = "character"),
9 make_option("--metadata", type = "character"),
10 make_option("--metadata_cols", type = "character"),
11 make_option("--metadata_cols_filter", type = "character"),
12 make_option("--adduct_split", action = "store_true"),
13 make_option("--xcms_groupids", type = "character"),
14 make_option("--filter", action = "store_true"),
15 make_option("--intensity_ra", type = "character"),
16 make_option("--include_adducts", type = "character"),
17 make_option("--msp_schema", type = "character"),
18 make_option("--include_adducts_custom", type = "character", default = ""),
19 make_option("--out_dir", type = "character", default = ".")
20 )
21 opt <- parse_args(OptionParser(option_list = option_list))
22
23 print(opt)
24
25 load(opt$rdata_input)
26
27 if (is.null(opt$metadata)) {
28 metadata <- NULL
29 }else{
30 metadata <- read.table(opt$metadata, header = TRUE, sep = "\t",
31 stringsAsFactors = FALSE, check.names = FALSE)
32
33 if (!opt$metadata_cols_filter == "") {
34 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]]
35
36 metadata <- metadata[, metadata_cols_filter, drop = FALSE]
37 print(metadata)
38
39 if (!"grpid" %in% colnames(metadata)) {
40 metadata$grpid <- seq_len(nrow(metadata))
41 }
42
43 print(metadata)
44
45 }
46
47 }
48
49
50
51 if (is.null(opt$metadata_cols) || opt$metadata_cols == "") {
52 metadata_cols <- NULL
53 }else{
54 metadata_cols <- opt$metadata_cols
55
56 }
57
58
59 if (is.null(opt$adduct_split)) {
60 adduct_split <- FALSE
61 }else{
62 adduct_split <- TRUE
63 }
64
65 if (is.null(opt$xcms_groupids)) {
66 xcms_groupids <- NULL
67 }else{
68 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]])
69 }
70
71
72 if (is.null(opt$include_adducts_custom)) {
73 include_adducts_custom <- ""
74 }else{
75 include_adducts_custom <- opt$include_adducts_custom
76 }
77
78
79 if (opt$include_adducts == "None") {
80 include_adducts <- ""
81 }else{
82 include_adducts <- opt$include_adducts
83 }
84
85 include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "")
86
87 include_adducts_all <- gsub("^,", "", include_adducts_all)
88 include_adducts_all <- gsub(",$", "", include_adducts_all)
89
90 include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
91 include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
92 include_adducts_all <- trimws(include_adducts_all)
93 include_adducts_all <- gsub(",", " ", include_adducts_all)
94
95
96
97 if (is.null(opt$filter)) {
98 filter <- FALSE
99 }else{
100 filter <- TRUE
101 }
102
103
104
105 msPurity::createMSP(pa,
106 msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"),
107 metadata = metadata,
108 metadata_cols = metadata_cols,
109 method = opt$method,
110 adduct_split = adduct_split,
111 xcms_groupids = xcms_groupids,
112 filter = filter,
113 intensity_ra = opt$intensity_ra,
114 include_adducts = include_adducts_all,
115 msp_schema = opt$msp_schema)
116
117 print("msp created")