annotate purityA.R @ 6:d4a17be5429a draft

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

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

option_list <- list(
  make_option(c("-o", "--out_dir"), type = "character"),
  make_option("--mzML_files", type = "character"),
  make_option("--galaxy_names", type = "character"),
  make_option("--minOffset", type = "numeric"),
  make_option("--maxOffset", type = "numeric"),
  make_option("--ilim", type = "numeric"),
  make_option("--iwNorm", default = "none", type = "character"),
  make_option("--exclude_isotopes", action = "store_true"),
  make_option("--isotope_matrix", type = "character"),
  make_option("--mostIntense", action = "store_true"),
  make_option("--plotP", action = "store_true"),
  make_option("--nearest", action = "store_true"),
  make_option("--cores", default = 4),
  make_option("--ppmInterp", default = 7)
)

opt <- parse_args(OptionParser(option_list = option_list))
print(opt)

if (opt$iwNorm == "none") {
    iwNorm <- FALSE
    iwNormFun <- NULL
}else if (opt$iwNorm == "gauss") {
    iwNorm <- TRUE
    if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
      print("User has to define offsets if using Gaussian normalisation")
    }else{
      iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset),
                                         maxOff = as.numeric(opt$maxOffset))
    }
}else if (opt$iwNorm == "rcosine") {
    iwNorm <- TRUE
    if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
      print("User has to define offsets if using R-cosine normalisation")
    }else{
      iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset),
                                           maxOff = as.numeric(opt$maxOffset))
    }
}else if (opt$iwNorm == "QE5") {
    iwNorm <- TRUE
    iwNormFun <- msPurity::iwNormQE.5()
}

filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]])
filepaths <- filepaths[filepaths != ""]



if (is.null(opt$minOffset) || is.null(opt$maxOffset)) {
    offsets <- NA
}else{
    offsets <- as.numeric(c(opt$minOffset, opt$maxOffset))
}


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

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

if (is.null(opt$plotP)) {
    plotP <- FALSE
    plotdir <- NULL
}else{
    plotP <- TRUE
    plotdir <- opt$out_dir
}


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

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

pa <- msPurity::purityA(filepaths,
                        cores = opt$cores,
                        mostIntense = mostIntense,
                        nearest = nearest,
                        offsets = offsets,
                        plotP = plotP,
                        plotdir = plotdir,
                        interpol = "linear",
                        iwNorm = iwNorm,
                        iwNormFun = iwNormFun,
                        ilim = opt$ilim,
                        mzRback = "pwiz",
                        isotopes = isotopes,
                        im = im,
                        ppmInterp = opt$ppmInterp)


if (!is.null(opt$galaxy_names)) {
    galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
    galaxy_names <- galaxy_names[galaxy_names != ""]
    names(pa@fileList) <- galaxy_names
}

print(pa)
save(pa, file = file.path(opt$out_dir, "purityA_output.RData"))

pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])

print(head(pa@puritydf))
write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t")