--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/purityA.R	Thu Mar 04 12:14:02 2021 +0000
@@ -0,0 +1,124 @@
+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")