--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dimsPredictPuritySingle.R	Thu Mar 04 12:17:52 2021 +0000
@@ -0,0 +1,160 @@
+library(msPurity)
+library(optparse)
+print(sessionInfo())
+
+option_list <- list(
+  make_option(c("--mzML_file"), type = "character"),
+  make_option(c("--mzML_files"), type = "character"),
+  make_option(c("--mzML_filename"), type = "character", default = ""),
+  make_option(c("--mzML_galaxy_names"), type = "character", default = ""),
+  make_option(c("--peaks_file"), type = "character"),
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option("--minoffset", default = 0.5),
+  make_option("--maxoffset", default = 0.5),
+  make_option("--ilim", default = 0.05),
+  make_option("--ppm", default = 4),
+  make_option("--dimspy", action = "store_true"),
+  make_option("--sim", action = "store_true"),
+  make_option("--remove_nas", action = "store_true"),
+  make_option("--iwNorm", default = "none", type = "character"),
+  make_option("--file_num_dimspy", default = 1),
+  make_option("--exclude_isotopes", action = "store_true"),
+  make_option("--isotope_matrix", type = "character")
+)
+
+# store options
+opt <- parse_args(OptionParser(option_list = option_list))
+
+print(sessionInfo())
+print(opt)
+
+print(opt$mzML_files)
+print(opt$mzML_galaxy_names)
+
+str_to_vec <- function(x) {
+    print(x)
+    x <- trimws(strsplit(x, ",")[[1]])
+    return(x[x != ""])
+}
+
+find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename) {
+    mzML_filename <- trimws(mzML_filename)
+    mzML_files <- str_to_vec(mzML_files)
+    galaxy_names <- str_to_vec(galaxy_names)
+    if (mzML_filename %in% galaxy_names) {
+        return(mzML_files[galaxy_names == mzML_filename])
+    }else{
+        stop(paste("mzML file not found - ", mzML_filename))
+    }
+}
+
+
+if (is.null(opt$dimspy)) {
+    df <- read.table(opt$peaks_file, header = TRUE, sep = "\t")
+    if (file.exists(opt$mzML_file)) {
+        mzML_file <- opt$mzML_file
+    }else if (!is.null(opt$mzML_files)) {
+        mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names,
+                                    opt$mzML_filename)
+    }else{
+        mzML_file <- file.path(opt$mzML_file, filename)
+    }
+}else{
+    indf <- read.table(opt$peaks_file,
+                       header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+
+    filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
+    print(filename)
+    # check if the data file is mzML or RAW (can only use mzML currently) so
+    # we expect an mzML file of the same name in the same folder
+    indf$i <- indf[, colnames(indf) == filename]
+    indf[, colnames(indf) == filename] <- as.numeric(indf[, colnames(indf) == filename])
+
+    filename <- sub("raw", "mzML", filename, ignore.case = TRUE)
+    print(filename)
+
+    if (file.exists(opt$mzML_file)) {
+        mzML_file <- opt$mzML_file
+    }else if (!is.null(opt$mzML_files)) {
+        mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename)
+    }else{
+        mzML_file <- file.path(opt$mzML_file, filename)
+    }
+
+    # Update the dimspy output with the correct information
+    df <- indf[4:nrow(indf), ]
+    if ("blank_flag" %in% colnames(df)) {
+        df <- df[df$blank_flag == 1, ]
+    }
+    colnames(df)[colnames(df) == "m.z"] <- "mz"
+
+    if ("nan" %in% df$mz) {
+        df[df$mz == "nan", ]$mz <- NA
+    }
+    df$mz <- as.numeric(df$mz)
+}
+
+if (!is.null(opt$remove_nas)) {
+  df <- df[!is.na(df$mz), ]
+}
+
+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$exclude_isotopes)) {
+    isotopes <- FALSE
+}else{
+    isotopes <- TRUE
+}
+
+if (is.null(opt$sim)) {
+    sim <- FALSE
+}else{
+    sim <- TRUE
+}
+
+minOffset <- as.numeric(opt$minoffset)
+maxOffset <- as.numeric(opt$maxoffset)
+
+if (opt$iwNorm == "none") {
+    iwNorm <- FALSE
+    iwNormFun <- NULL
+}else if (opt$iwNorm == "gauss") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormGauss(minOff = -minOffset, maxOff = maxOffset)
+}else if (opt$iwNorm == "rcosine") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormRcosine(minOff = -minOffset, maxOff = maxOffset)
+}else if (opt$iwNorm == "QE5") {
+    iwNorm <- TRUE
+    iwNormFun <- msPurity::iwNormQE.5()
+}
+
+print("FIRST ROWS OF PEAK FILE")
+print(head(df))
+print(mzML_file)
+predicted <- msPurity::dimsPredictPuritySingle(df$mz,
+                                     filepth = mzML_file,
+                                     minOffset = minOffset,
+                                     maxOffset = maxOffset,
+                                     ppm = opt$ppm,
+                                     mzML = TRUE,
+                                     sim = sim,
+                                     ilim = opt$ilim,
+                                     isotopes = isotopes,
+                                     im = im,
+                                     iwNorm = iwNorm,
+                                     iwNormFun = iwNormFun
+                                     )
+predicted <- cbind(df, predicted)
+
+print(head(predicted))
+print(file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"))
+
+write.table(predicted,
+            file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"),
+            row.names = FALSE, sep = "\t")