Mercurial > repos > computational-metabolomics > mspurity_purityx
view combineAnnotations.R @ 0:a141be614e76 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author | computational-metabolomics |
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date | Wed, 27 Nov 2019 12:41:53 -0500 |
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children | d7c5fa406ea8 |
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library(optparse) library(msPurity) print(sessionInfo()) # Get the parameter option_list <- list( make_option(c("-s","--sm_resultPth"),type="character"), make_option(c("-m","--metfrag_resultPth"),type="character"), make_option(c("-c","--sirius_csi_resultPth"),type="character"), make_option(c("-p","--probmetab_resultPth"),type="character"), make_option(c("-l","--ms1_lookup_resultPth"),type="character"), make_option("--ms1_lookup_checkAdducts", action="store_true"), make_option("--ms1_lookup_keepAdducts", type="character", default=NA), make_option("--ms1_lookup_dbSource", type="character", default="hmdb"), make_option("--sm_weight", type="numeric"), make_option("--metfrag_weight", type="numeric"), make_option("--sirius_csi_weight", type="numeric"), make_option("--probmetab_weight", type="numeric"), make_option("--ms1_lookup_weight", type="numeric"), make_option("--biosim_weight", type="numeric"), make_option("--create_new_database", action="store_true"), make_option("--outdir", type="character", default="."), make_option("--compoundDbType", type="character", default="sqlite"), make_option("--compoundDbPth", type="character", default=NA), make_option("--compoundDbHost", type="character", default=NA) ) opt <- parse_args(OptionParser(option_list=option_list)) print(opt) if (!is.null(opt$create_new_database)){ sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite') file.copy(opt$sm_resultPth, sm_resultPth) }else{ sm_resultPth <- opt$sm_resultPth } if (is.null(opt$ms1_lookup_checkAdducts)){ opt$ms1_lookup_checkAdducts <- FALSE } if (!is.null(opt$ms1_lookup_keepAdducts)){ opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts) opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts) ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]] } weights <-list('sm'=opt$sm_weight, 'metfrag'=opt$metfrag_weight, 'sirius_csifingerid'= opt$sirius_csi_weight, 'probmetab'=opt$probmetab_weight, 'ms1_lookup'=opt$ms1_lookup_weight, 'biosim'=opt$biosim_weight ) print(weights) if (round(!sum(unlist(weights),0)==1)){ stop(paste0('The weights should sum to 1 not ', sum(unlist(weights)))) } if (opt$compoundDbType=='local_config'){ # load in compound config # Soure local function taken from workflow4metabolomics source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } source_local("dbconfig.R") }else{ compoundDbPth = opt$compoundDbPth compoundDbType = opt$compoundDbType compoundDbName = NA compoundDbHost = NA compoundDbPort = NA compoundDbUser = NA compoundDbPass = NA } summary_output <- msPurity::combineAnnotations( sm_resultPth = sm_resultPth, compoundDbPth = compoundDbPth, metfrag_resultPth = opt$metfrag_resultPth, sirius_csi_resultPth = opt$sirius_csi_resultPth, probmetab_resultPth = opt$probmetab_resultPth, ms1_lookup_resultPth = opt$ms1_lookup_resultPth, ms1_lookup_keepAdducts = ms1_lookup_keepAdducts, ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts, compoundDbType = compoundDbType, compoundDbName = compoundDbName, compoundDbHost = compoundDbHost, compoundDbPort = compoundDbPort, compoundDbUser = compoundDbUser, compoundDbPass = compoundDbPass, weights = weights) write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) closeAllConnections()