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comparison combineAnnotations.R @ 0:e96082a25ff0 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author computational-metabolomics
date Wed, 27 Nov 2019 13:42:05 -0500
parents
children 379b5c1dbe19
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-1:000000000000 0:e96082a25ff0
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("--create_new_database", action="store_true"),
25 make_option("--outdir", type="character", default="."),
26
27 make_option("--compoundDbType", type="character", default="sqlite"),
28 make_option("--compoundDbPth", type="character", default=NA),
29 make_option("--compoundDbHost", type="character", default=NA)
30 )
31 opt <- parse_args(OptionParser(option_list=option_list))
32
33 print(opt)
34
35 if (!is.null(opt$create_new_database)){
36 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
37 file.copy(opt$sm_resultPth, sm_resultPth)
38 }else{
39 sm_resultPth <- opt$sm_resultPth
40 }
41
42 if (is.null(opt$ms1_lookup_checkAdducts)){
43 opt$ms1_lookup_checkAdducts <- FALSE
44 }
45 if (!is.null(opt$ms1_lookup_keepAdducts)){
46 opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
47 opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
48 ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
49 }
50
51 weights <-list('sm'=opt$sm_weight,
52 'metfrag'=opt$metfrag_weight,
53 'sirius_csifingerid'= opt$sirius_csi_weight,
54 'probmetab'=opt$probmetab_weight,
55 'ms1_lookup'=opt$ms1_lookup_weight,
56 'biosim'=opt$biosim_weight
57 )
58 print(weights)
59 if (round(!sum(unlist(weights),0)==1)){
60
61 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
62 }
63
64 if (opt$compoundDbType=='local_config'){
65 # load in compound config
66 # Soure local function taken from workflow4metabolomics
67 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
68 source_local("dbconfig.R")
69 }else{
70 compoundDbPth = opt$compoundDbPth
71 compoundDbType = opt$compoundDbType
72 compoundDbName = NA
73 compoundDbHost = NA
74 compoundDbPort = NA
75 compoundDbUser = NA
76 compoundDbPass = NA
77 }
78
79
80
81 summary_output <- msPurity::combineAnnotations(
82 sm_resultPth = sm_resultPth,
83 compoundDbPth = compoundDbPth,
84 metfrag_resultPth = opt$metfrag_resultPth,
85 sirius_csi_resultPth = opt$sirius_csi_resultPth,
86 probmetab_resultPth = opt$probmetab_resultPth,
87 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
88 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
89 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
90
91 compoundDbType = compoundDbType,
92 compoundDbName = compoundDbName,
93 compoundDbHost = compoundDbHost,
94 compoundDbPort = compoundDbPort,
95 compoundDbUser = compoundDbUser,
96 compoundDbPass = compoundDbPass,
97 weights = weights)
98
99 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
100
101
102 closeAllConnections()
103