Program.cs

using System;
using System.Diagnostics;
using Newtonsoft.Json;

/// <summary>
/// A C# command line tool extracting the meta data from one or more raw files and putting them in a useful shaped json file.
///
/// Due to the design of the RawFileReader (RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc.) it is running as 64 bit code on Windows only. 
/// Compiled in Visual Studio Community 2017 (Version 15.8.7, .net 4.7.03056) on Windows 10 64 bit it was tested for the following Instruments: 
/// Thermo EASY-nLC, Q Exactive Plus - Orbitrap MS, Q Exactive HF - Orbitrap MS, Q Exactive - Orbitrap MS, LTQ Orbitrap Velos MS, Orbitrap Fusion.
/// </summary>

namespace MARMoSET
{
    public class Program
    {
        /// <summary>
        /// The main routine for this program. It takes a raw file or a directory with raw files as first argument.
        /// Then collects their meta data, groups them in a FileSet and writes a JSON file as output, depending on the second argument.
        /// </summary>
        /// <param name="args"> The command line arguments for this program.  
        ///     The RAW file name or directory should be passed as the first argument. 
        ///     Optionaly the output path as the second.</param>
        /// 
        public static void Main(string[] args)
        {
            // checking time
            Stopwatch watch = new Stopwatch();
            watch.Start();

            // local variable to check if the output was supplied as an argument to the program
            bool consoleOut = false;
            bool pathShort = false;

            string path = string.Empty;
            if (args.Length > 0)
            {  
                path = args[0];
            }
            // check if the first argument was supplied
            if (string.IsNullOrEmpty(path))
            {
                Console.WriteLine("No path specified!");
            }

            // help
            else if (path.Equals("-h") || path.Equals("-H"))
            {
                Console.WriteLine(
                    "\n" +
                    "  MARMoSET is extracting the meta data from one or more raw files and putting them in a useful shaped JSON file.\n\n" +
                    "   Usage:\n\n" +
                    "  MARMoSET.exe [input path] [jsonfile name]\n\n" +
                    "       input path :  You can specify either a path to a single raw file or a path to a directory containing one or multiple raw files.\n" +
                    "       jsonfile name  :  You can set an outputfile(.json). It will be saved in the same directory as the input files.\n" +
                    "       For saving with full path set -r in front. If empty the output will be send to the standard output."
                    );
            }

            else
            {
                // Output path
                string outName = string.Empty;
                if (args.Length > 1)
                {   // 2nd argument is path + name
                    outName = args[1];
                    if (outName.Equals("-r") || outName.Equals("-R")) // Mode for R Package
                    {
                        pathShort = true;
                        outName = args[2];
                    }
                }

                if (string.IsNullOrEmpty(outName))
                {   // no 2nd arg -> file on console
                    consoleOut = true;
                }
               
            //___________________________________________________
            // main file handling:
                var rawFiles = new FileSet(path, consoleOut);
                // convert structure to JSON
                string json = JsonConvert.SerializeObject(rawFiles, Formatting.Indented) + "\n";
                // deleting ":" at the end of keys (tune data and instrument method)
                json = json.Replace(":\":", "\":");

                string outPath;
                string fullOutPath;
                // write to standard out or to file
                if (consoleOut)
                {
                    Console.WriteLine(json);
                }
                else
                {
                    if (pathShort)
                    {
                        fullOutPath = outName;
                    }
                    else
                    {
                        // is path to dir or file?
                        string lowPath = path.ToLower();
                        if (lowPath.EndsWith(".raw"))
                        {
                            outPath = (System.IO.Path.GetDirectoryName(path));
                        }
                        else
                        {
                            outPath = path;
                        }
                        fullOutPath = System.IO.Path.Combine(outPath, outName);
                    }
                    System.IO.File.WriteAllText(fullOutPath, json);
                }

                // print time spend
                watch.Stop();
                if (!consoleOut)
                {
                    Console.WriteLine("Time spent: " + watch.Elapsed);
                }
            }
        }
    }
}