Mercurial > repos > tomnl > mspurity_flagremove

comparison spectralMatching.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 7e4a5ce0877d
children b71677d4f958
comparison
equal deleted inserted replaced
11:7e4a5ce0877d 12:2c8b5a640a04
1 library(msPurity) 1 library(msPurity)
2 library(msPurityData) 2 library(msPurityData)
3 library(optparse) 3 library(optparse)
4 print(sessionInfo()) 4 print(sessionInfo())
5 5 # load in library spectra config
6 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
7 source_local("dbconfig.R")
6 8
7 option_list <- list( 9 option_list <- list(
8 make_option(c("-o", "--outDir"), type="character"), 10 make_option(c("-o", "--outDir"), type="character"),
9 make_option("--q_dbPth", type="character"), 11 make_option("--q_dbPth", type="character"),
10 make_option("--l_dbPth", type="character"), 12 make_option("--l_dbPth", type="character"),
13
14 make_option("--q_dbType", type="character", default=NA),
15 make_option("--l_dbType", type="character", default=NA),
11 16
12 make_option("--q_msp", type="character", default=NA), 17 make_option("--q_msp", type="character", default=NA),
13 make_option("--l_msp", type="character", default=NA), 18 make_option("--l_msp", type="character", default=NA),
14 19
15 make_option("--q_defaultDb", action="store_true"), 20 make_option("--q_defaultDb", action="store_true"),
96 101
97 } 102 }
98 103
99 if(!is.null(opt$q_defaultDb)){ 104 if(!is.null(opt$q_defaultDb)){
100 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") 105 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
101 }else if (!is.null(opt$q_dbPth)){ 106 q_dbType <- 'sqlite'
107 }else if (!opt$q_dbType=='local_config'){
108 q_dbType <- opt$q_dbType
102 q_dbPth <- opt$q_dbPth 109 q_dbPth <- opt$q_dbPth
103 }else{
104 message('No query database available')
105 exit()
106 } 110 }
107 111
108 if(!is.null(opt$l_defaultDb)){ 112 if(!is.null(opt$l_defaultDb)){
109 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") 113 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
110 }else if (!is.null(opt$l_dbPth)){ 114 l_dbType <- 'sqlite'
115 }else if (!opt$l_dbType=='local_config'){
116 l_dbType <- opt$l_dbType
111 l_dbPth <- opt$l_dbPth 117 l_dbPth <- opt$l_dbPth
112 }else{ 118 }
113 message('No library database available') 119
114 exit() 120
115 }
116 121
117 122
118 q_polarity <- extractMultiple(opt$q_polarity) 123 q_polarity <- extractMultiple(opt$q_polarity)
119 l_polarity <- extractMultiple(opt$l_polarity) 124 l_polarity <- extractMultiple(opt$l_polarity)
120 125
188 q_rtrangeMin <- NA 193 q_rtrangeMin <- NA
189 } 194 }
190 195
191 196
192 197
193 sm <- msPurity::spectralMatching(q_dbPth = q_dbPth, 198 sm <- msPurity::spectralMatching(
194 l_dbPth = l_dbPth,
195
196 q_purity = opt$q_purity, 199 q_purity = opt$q_purity,
197 l_purity = opt$l_purity, 200 l_purity = opt$l_purity,
198 201
199 q_ppmProd = opt$q_ppmProd, 202 q_ppmProd = opt$q_ppmProd,
200 l_ppmProd = opt$l_ppmProd, 203 l_ppmProd = opt$l_ppmProd,
234 rttol=opt$rttol, 237 rttol=opt$rttol,
235 cores=opt$cores, 238 cores=opt$cores,
236 239
237 copyDb=copyDb, 240 copyDb=copyDb,
238 updateDb=updateDb, 241 updateDb=updateDb,
239 outPth = "db_with_spectral_matching.sqlite" 242 outPth = "db_with_spectral_matching.sqlite",
243
244 q_dbPth = q_dbPth,
245 q_dbType = q_dbType,
246 q_dbName = q_dbName,
247 q_dbHost = q_dbHost,
248 q_dbUser = q_dbUser,
249 q_dbPass = q_dbPass,
250 q_dbPort = q_dbPort,
251
252 l_dbPth = l_dbPth,
253 l_dbType = l_dbType,
254 l_dbName = l_dbName,
255 l_dbHost = l_dbHost,
256 l_dbUser = l_dbUser,
257 l_dbPass = l_dbPass,
258 l_dbPort = l_dbPort
259
240 ) 260 )
241 261
242 262
243 263
244 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) 264 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)