view createMSP.R @ 3:59c1f9077c3b draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db

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

# Get the parameter
option_list <- list(
  make_option(c("-i","--rdata_input"),type="character"),
  make_option(c("-m","--method"),type="character"),
  make_option(c("-meta","--metadata"),type="character"),
  make_option(c("-metac","--metadata_cols"),type="character"),
  make_option(c("-a","--adduct_split"),type="character"),
  make_option(c("-x","--xcms_groupids"),type="character"),
  make_option(c("-f","--filter"),action="store_true"),
  make_option("--intensity_ra",type="character"),
  make_option("--msp_schema",type="character"),
  make_option(c("-o","--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)
  print(head(metadata))
}

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$filter)){
  filter <- FALSE
}else{
  filter <- TRUE
}

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

print('msp created')