--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mzXMLShaper.R	Mon Oct 07 11:40:19 2024 +0000
@@ -0,0 +1,46 @@
+#!/usr/bin/env Rscript
+
+# R version 4.3.3
+# Conversion tool mzXMLShaper.R (former cdf2mzml)
+# Author: Quentin RUIN
+# Creation date: 25/04/2023
+# Last updated: 09/09/2024
+
+cat("\nJob starting time:\n", format(Sys.time(), "%a %d %b %Y %X"), "\n\n")
+
+library(mzR)
+library(msdata)
+library("W4MRUtils")
+library("tools")
+
+args <- W4MRUtils::parse_args(args = commandArgs())
+
+cat("\n\n--------------------------------------------------------------------",
+    "\nParameters used by the 'mz(X)MLShaper' tool:\n\n")
+cat("--------------------------------------------------------------------\n\n")
+print(args)
+
+inputfilename <- args[[1]]
+outputfileformat <- args[[2]]
+outputfilename <- args[[3]]
+spectrum <- mzR::openMSfile(inputfilename)
+
+## Get the spectra
+pks <- mzR::spectra(spectrum)
+
+## Get the header
+hdr <- mzR::header(spectrum)
+
+if (outputfileformat == "mzml") {
+  writeMSData(pks, file = outputfilename, outformat = "mzml", header = hdr)
+}
+
+if (outputfileformat == "mzXml") {
+  writeMSData(pks, file = outputfilename, outformat = "mzxml", header = hdr)
+}
+
+cat("\n--------------------------------------------------------------------",
+    "\nInformation about R (version, Operating System, attached or loaded packages):\n\n")
+sessionInfo()
+cat("--------------------------------------------------------------------\n",
+    "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X"))