annotate combineAnnotations.R @ 11:416460f611cc draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 94f746247c464fb270358421399810d8a9fb9e8a

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()