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comparison combineAnnotations.R @ 12:2c8b5a640a04 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:49:43 -0400
parents 1a77ed3c94b7
children 2445754177bb
comparison
equal deleted inserted replaced
11:7e4a5ce0877d 12:2c8b5a640a04
6 option_list <- list( 6 option_list <- list(
7 make_option(c("-s","--sm_resultPth"),type="character"), 7 make_option(c("-s","--sm_resultPth"),type="character"),
8 make_option(c("-m","--metfrag_resultPth"),type="character"), 8 make_option(c("-m","--metfrag_resultPth"),type="character"),
9 make_option(c("-c","--sirius_csi_resultPth"),type="character"), 9 make_option(c("-c","--sirius_csi_resultPth"),type="character"),
10 make_option(c("-p","--probmetab_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
11 make_option(c("-sw","--sm_weight"),type="numeric"), 17 make_option(c("-sw","--sm_weight"),type="numeric"),
12 make_option(c("-mw","--metfrag_weight"),type="numeric"), 18 make_option(c("-mw","--metfrag_weight"),type="numeric"),
13 make_option(c("-cw","--sirius_csi_weight"),type="numeric"), 19 make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
14 make_option(c("-pw","--probmetab_weight"),type="numeric"), 20 make_option(c("-pw","--probmetab_weight"),type="numeric"),
21 make_option(c("-lw","--ms1_lookup_weight"),type="numeric"),
22 make_option(c("-bw","--biosim_weight"),type="numeric"),
23
15 make_option("--create_new_database", action="store_true"), 24 make_option("--create_new_database", action="store_true"),
16 make_option(c("-o","--outdir"),type="character", default="."), 25 make_option(c("-o","--outdir"),type="character", default="."),
17 make_option("--eic", action="store_true") 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)
18 ) 30 )
19 opt <- parse_args(OptionParser(option_list=option_list)) 31 opt <- parse_args(OptionParser(option_list=option_list))
20 32
21 print(opt) 33 print(opt)
22 34
25 file.copy(opt$sm_resultPth, sm_resultPth) 37 file.copy(opt$sm_resultPth, sm_resultPth)
26 }else{ 38 }else{
27 sm_resultPth <- opt$sm_resultPth 39 sm_resultPth <- opt$sm_resultPth
28 } 40 }
29 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 }
30 50
31 weights <-list('sm'=opt$sm_weight, 51 weights <-list('sm'=opt$sm_weight,
32 'metfrag'=opt$metfrag_weight, 52 'metfrag'=opt$metfrag_weight,
33 'sirius_csifingerid'= opt$sirius_csi_weight, 53 'sirius_csifingerid'= opt$sirius_csi_weight,
34 'probmetab'=opt$probmetab_weight 54 'probmetab'=opt$probmetab_weight,
55 'ms1_lookup'=opt$ms1_lookup_weight,
56 'biosim'=opt$biosim_weight
35 ) 57 )
36 58 print(weights)
37 if (round(!sum(unlist(weights),0)==1)){ 59 if (round(!sum(unlist(weights),0)==1)){
38 60
39 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights)))) 61 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
40 } 62 }
41 63
42 summary_output <- msPurity::combineAnnotations(sm_resultPth, 64 if (opt$compoundDbType=='local_config'){
43 opt$metfrag_resultPth, 65 # load in compound config
44 opt$sirius_csi_resultPth, 66 # Soure local function taken from workflow4metabolomics
45 opt$probmetab_resultPth, 67 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
46 weights = weights) 68 source_local("dbconfig.R")
69 }else{
70 compoundDbType = opt$compoundDbType
71 compoundDbName = NA
72 compoundDbHost = NA
73 compoundDbPort = NA
74 compoundDbUser = NA
75 compoundDbPass = NA
76 }
77
78
79
80 summary_output <- msPurity::combineAnnotations(
81 sm_resultPth = sm_resultPth,
82 compoundDbPth = opt$compoundDbPth,
83 metfrag_resultPth = opt$metfrag_resultPth,
84 sirius_csi_resultPth = opt$sirius_csi_resultPth,
85 probmetab_resultPth = opt$probmetab_resultPth,
86 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
87 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
88 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
89
90 compoundDbType = compoundDbType,
91 compoundDbName = compoundDbName,
92 compoundDbHost = compoundDbHost,
93 compoundDbPort = compoundDbPort,
94 compoundDbUser = compoundDbUser,
95 compoundDbPass = compoundDbPass,
96 weights = weights)
47 97
48 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) 98 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
49 99
50 100
51 closeAllConnections() 101 closeAllConnections()