annotate createMSP.R @ 6:a67b129cd78e draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"

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")