Mercurial > repos > computational-metabolomics > mspurity_puritya
view combineAnnotations.R @ 11:416460f611cc draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 94f746247c464fb270358421399810d8a9fb9e8a
author | computational-metabolomics |
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date | Fri, 13 Sep 2024 13:42:16 +0000 |
parents | 33d733850e85 |
children |
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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("--summaryOutput", action = "store_true"), 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 (is.null(opt$probmetab_resultPth)) { opt$probmetab_resultPth <- NA } if (round(!sum(unlist(weights), 0) == 1)) { stop(paste0("The weights should sum to 1 not ", sum(unlist(weights)))) } if (is.null(opt$summaryOutput)) { summaryOutput <- FALSE } else { summaryOutput <- TRUE } if (opt$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$ms1_lookup_checkAdducts, compoundDbType = compoundDbType, compoundDbName = compoundDbName, compoundDbHost = compoundDbHost, compoundDbPort = compoundDbPort, compoundDbUser = compoundDbUser, compoundDbPass = compoundDbPass, weights = weights, summaryOutput = summaryOutput ) if (summaryOutput) { write.table(summary_output, file.path(opt$outdir, "combined_annotations.tsv"), sep = "\t", row.names = FALSE ) } write.table(summary_output, file.path(opt$outdir, "combined_annotations.tsv"), sep = "\t", row.names = FALSE ) closeAllConnections()