--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combineAnnotations.R	Thu Mar 04 12:14:02 2021 +0000
@@ -0,0 +1,123 @@
+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()