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comparison combineAnnotations.R @ 0:353d48ece635 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 12:17:52 +0000
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-1:000000000000 0:353d48ece635
1 library(optparse)
2 library(msPurity)
3 print(sessionInfo())
4
5 # Get the parameter
6 option_list <- list(
7 make_option(c("-s", "--sm_resultPth"), type = "character"),
8 make_option(c("-m", "--metfrag_resultPth"), type = "character"),
9 make_option(c("-c", "--sirius_csi_resultPth"), type = "character"),
10 make_option(c("-p", "--probmetab_resultPth"), type = "character"),
11 make_option(c("-l", "--ms1_lookup_resultPth"), type = "character"),
12
13 make_option("--ms1_lookup_checkAdducts", action = "store_true"),
14 make_option("--ms1_lookup_keepAdducts", type = "character", default = NA),
15 make_option("--ms1_lookup_dbSource", type = "character", default = "hmdb"),
16
17 make_option("--sm_weight", type = "numeric"),
18 make_option("--metfrag_weight", type = "numeric"),
19 make_option("--sirius_csi_weight", type = "numeric"),
20 make_option("--probmetab_weight", type = "numeric"),
21 make_option("--ms1_lookup_weight", type = "numeric"),
22 make_option("--biosim_weight", type = "numeric"),
23
24 make_option("--summaryOutput", action = "store_true"),
25
26 make_option("--create_new_database", action = "store_true"),
27 make_option("--outdir", type = "character", default = "."),
28
29 make_option("--compoundDbType", type = "character", default = "sqlite"),
30 make_option("--compoundDbPth", type = "character", default = NA),
31 make_option("--compoundDbHost", type = "character", default = NA)
32 )
33 opt <- parse_args(OptionParser(option_list = option_list))
34
35 print(opt)
36
37 if (!is.null(opt$create_new_database)) {
38 sm_resultPth <- file.path(opt$outdir, "combined_annotations.sqlite")
39 file.copy(opt$sm_resultPth, sm_resultPth)
40 }else{
41 sm_resultPth <- opt$sm_resultPth
42 }
43
44 if (is.null(opt$ms1_lookup_checkAdducts)) {
45 opt$ms1_lookup_checkAdducts <- FALSE
46 }
47 if (!is.null(opt$ms1_lookup_keepAdducts)) {
48 opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
49 opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
50 ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
51 }
52
53 weights <- list("sm" = opt$sm_weight,
54 "metfrag" = opt$metfrag_weight,
55 "sirius_csifingerid" = opt$sirius_csi_weight,
56 "probmetab" = opt$probmetab_weight,
57 "ms1_lookup" = opt$ms1_lookup_weight,
58 "biosim" = opt$biosim_weight
59 )
60 print(weights)
61
62 if (is.null(opt$probmetab_resultPth)) {
63 opt$probmetab_resultPth <- NA
64 }
65
66 if (round(!sum(unlist(weights), 0) == 1)) {
67 stop(paste0("The weights should sum to 1 not ", sum(unlist(weights))))
68 }
69
70 if (is.null(opt$summaryOutput)) {
71 summaryOutput <- FALSE
72 }else{
73 summaryOutput <- TRUE
74 }
75
76 if (opt$compoundDbType == "local_config") {
77 # load in compound config
78 # Soure local function taken from workflow4metabolomics
79 source_local <- function(fname) {
80 argv <- commandArgs(trailingOnly = FALSE)
81 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
82 source(paste(base_dir, fname, sep = "/"))
83 }
84 source_local("dbconfig.R")
85 }else{
86 compoundDbPth <- opt$compoundDbPth
87 compoundDbType <- opt$compoundDbType
88 compoundDbName <- NA
89 compoundDbHost <- NA
90 compoundDbPort <- NA
91 compoundDbUser <- NA
92 compoundDbPass <- NA
93 }
94
95 summary_output <- msPurity::combineAnnotations(
96 sm_resultPth = sm_resultPth,
97 compoundDbPth = compoundDbPth,
98 metfrag_resultPth = opt$metfrag_resultPth,
99 sirius_csi_resultPth = opt$sirius_csi_resultPth,
100 probmetab_resultPth = opt$probmetab_resultPth,
101 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
102 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
103 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
104
105 compoundDbType = compoundDbType,
106 compoundDbName = compoundDbName,
107 compoundDbHost = compoundDbHost,
108 compoundDbPort = compoundDbPort,
109 compoundDbUser = compoundDbUser,
110 compoundDbPass = compoundDbPass,
111 weights = weights,
112 summaryOutput = summaryOutput)
113 if (summaryOutput) {
114 write.table(summary_output,
115 file.path(opt$outdir, "combined_annotations.tsv"),
116 sep = "\t", row.names = FALSE)
117 }
118
119 write.table(summary_output,
120 file.path(opt$outdir, "combined_annotations.tsv"),
121 sep = "\t", row.names = FALSE)
122
123 closeAllConnections()