annotate createMSP.R @ 10:f5043704dd62 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5

library(optparse)
library(msPurity)
print(sessionInfo())

# Get the parameter
option_list <- list(
  make_option("--rdata_input", type = "character"),
  make_option("--method", type = "character"),
  make_option("--metadata", type = "character"),
  make_option("--metadata_cols", type = "character"),
  make_option("--metadata_cols_filter", type = "character"),
  make_option("--adduct_split", action = "store_true"),
  make_option("--xcms_groupids", type = "character"),
  make_option("--filter", action = "store_true"),
  make_option("--intensity_ra", type = "character"),
  make_option("--include_adducts", type = "character"),
  make_option("--msp_schema", type = "character"),
  make_option("--include_adducts_custom", type = "character", default = ""),
  make_option("--out_dir", type = "character", default = ".")
)
opt <- parse_args(OptionParser(option_list = option_list))

print(opt)

load(opt$rdata_input)

if (is.null(opt$metadata)) {
  metadata <- NULL
} else {
  metadata <- read.table(opt$metadata,
    header = TRUE, sep = "\t",
    stringsAsFactors = FALSE, check.names = FALSE
  )

  if (!opt$metadata_cols_filter == "") {
    metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]]

    metadata <- metadata[, metadata_cols_filter, drop = FALSE]
    print(metadata)

    if (!"grpid" %in% colnames(metadata)) {
      metadata$grpid <- seq_len(nrow(metadata))
    }

    print(metadata)
  }
}



if (is.null(opt$metadata_cols) || opt$metadata_cols == "") {
  metadata_cols <- NULL
} else {
  metadata_cols <- opt$metadata_cols
}


if (is.null(opt$adduct_split)) {
  adduct_split <- FALSE
} else {
  adduct_split <- TRUE
}

if (is.null(opt$xcms_groupids)) {
  xcms_groupids <- NULL
} else {
  xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]])
}


if (is.null(opt$include_adducts_custom)) {
  include_adducts_custom <- ""
} else {
  include_adducts_custom <- opt$include_adducts_custom
}


if (opt$include_adducts == "None") {
  include_adducts <- ""
} else {
  include_adducts <- opt$include_adducts
}

include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "")

include_adducts_all <- gsub("^,", "", include_adducts_all)
include_adducts_all <- gsub(",$", "", include_adducts_all)

include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
include_adducts_all <- trimws(include_adducts_all)
include_adducts_all <- gsub(",", " ", include_adducts_all)



if (is.null(opt$filter)) {
  filter <- FALSE
} else {
  filter <- TRUE
}



msPurity::createMSP(pa,
  msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"),
  metadata = metadata,
  metadata_cols = metadata_cols,
  method = opt$method,
  adduct_split = adduct_split,
  xcms_groupids = xcms_groupids,
  filter = filter,
  intensity_ra = opt$intensity_ra,
  include_adducts = include_adducts_all,
  msp_schema = opt$msp_schema
)

print("msp created")