Merge branch 'eubic2020hackathon' of https://github.com/compomics/ThermoRawFileParser into eubic2020hackathon

Author: edeutsch

MainClass.cs

@@ -1,4 +1,5 @@
 using System;
+using System.Reflection;
 using System.IO;
 using log4net;
 using log4net.Core;
@@ -479,7 +480,10 @@ private static void RegularParametersParsing(string[] args)
 
                 if (help)
                 {
-                    ShowHelp("usage is (use -option=value for the optional arguments):", null,
+                    string helpmessage = String.Format("usage is {0} [subcommand] [options]\nsubcommand is xic|query\n",
+                        Assembly.GetExecutingAssembly().GetName().Name);
+                    ShowHelp(helpmessage +
+                        "(use -option=value for the optional arguments):", null,
                         optionSet);
                     return;
                 }

README.md

@@ -26,7 +26,9 @@ For running on Windows, omit `mono`. The optional parameters only work in the -o
 
 ```
 ThermoRawFileParser.exe --help
- usage is (use -option=value for the optional arguments):
+ usage is ThermoRawFileParser [subcommand] [option]
+ subcommand is xic|query
+ (use -option=value for the optional arguments):
   -h, --help                 Prints out the options.
       --version              Prints out the library version.
   -i, --input=VALUE          The raw file input (Required). Specify this or an