Unify command line arguments

Unify command line parameters for all modes and update the readme accordingly

Author: caetera

MainClass.cs

@@ -63,15 +63,15 @@ private static void XicParametersParsing(string[] args)
                     "h|help", "Prints out the options.",
                     h => parameters.help = h != null
                 },
+                {
+                    "i=|input=", "The raw file input (Required). Specify this or an input directory -d",
+                    v => singleFile = v
+                },
                 {
                     "d=|input_directory=",
                     "The directory containing the raw files (Required). Specify this or an input file -i.",
                     v => fileDirectory = v
                 },
-                {
-                    "i=|input=", "The raw file input (Required). Specify this or an input directory -d",
-                    v => singleFile = v
-                },
                 {
                     "j=|json=",
                     "The json input file (Required).",
@@ -82,16 +82,16 @@ private static void XicParametersParsing(string[] args)
                     "Show a json input file example.",
                     v => parameters.printJsonExample = v != null
                 },
-                {
-                    "o=|output_directory=",
-                    "The output directory. Specify this or an output file. Specifying neither writes to the input directory.",
-                    v => outputDirectory = v
-                },
                 {
                     "b=|output=",
                     "The output file. Specify this or an output directory. Specifying neither writes to the input directory.",
                     v => outputFile = v
                 },
+                {
+                    "o=|output_directory=",
+                    "The output directory. Specify this or an output file. Specifying neither writes to the input directory.",
+                    v => outputDirectory = v
+                },
                 {
                     "6|base64",
                     "Encodes the content of the xic vectors as base 64 encoded string.",
@@ -338,7 +338,7 @@ private static void SpectrumQueryParametersParsing(string[] args)
                     v => parameters.scans = v
                 },
                 {
-                    "b=|output_file",
+                    "b=|output=",
                     "The output file. Specifying none writes the output file to the input file parent directory.",
                     v => parameters.outputFile = v
                 },
@@ -510,15 +510,15 @@ private static void RegularParametersParsing(string[] args)
                     v => parseInput.RawDirectoryPath = v
                 },
                 {
-                    "o=|output=",
-                    "The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
-                    v => parseInput.OutputDirectory = v
-                },
-                {
-                    "b=|output_file",
+                    "b=|output=",
                     "The output file. Specify this or an output directory -o. Specifying neither writes to the input directory.",
                     v => parseInput.OutputFile = v
                 },
+                {
+                    "o=|output_directory=",
+                    "The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
+                    v => parseInput.OutputDirectory = v
+                },
                 {
                     "s|stdout",
                     "Write to standard output. Cannot be combined with file or directory output. Implies silent logging, i.e. logging level 0",

README.md

@@ -59,12 +59,13 @@ optional subcommands are xic|query (use [subcommand] -h for more info]):
   -d, --input_directory=VALUE
                              The directory containing the raw files (Required).
                                Specify this or an input raw file -i.
-  -o, --output=VALUE         The output directory. Specify this or an output
-                               file -b. Specifying neither writes to the input
-                               directory.
-  -b, --output_file=VALUE    The output file. Specify this or an output
+  -b, --output=VALUE    	 The output file. Specify this or an output
                                directory -o. Specifying neither writes to the
                                input directory.
+  -o, --output_directory=VALUE
+							 The output directory. Specify this or an output
+                               file -b. Specifying neither writes to the input
+                               directory.
   -s, --stdout               Write to standard output. Cannot be combined with
                                file or directory output. Implies silent logging,
                                 i.e. logging level 0
@@ -137,7 +138,7 @@ usage is:
   -h, --help                 Prints out the options.
   -i, --input=VALUE          The raw file input (Required).
   -n, --scans=VALUE          The scan numbers. e.g. "1-5, 20, 25-30"
-  -b, --output_file=VALUE    The output file. Specifying none writes the output
+  -b, --output=VALUE    	 The output file. Specifying none writes the output
                                file to the input file parent directory.
   -p, --noPeakPicking        Don't use the peak picking provided by the native
                                Thermo library. By default peak picking is
@@ -169,12 +170,13 @@ ThermoRawFileParser.exe xic --help
                                Specify this or an input file -i.
   -j, --json=VALUE           The json input file (Required).
   -p, --print_example        Show a json input file example.
-  -o, --output=VALUE         The output directory. Specify this or an output
-                               file. Specifying neither writes to the input
-                               directory.
-  -b, --output_file=VALUE    The output file. Specify this or an output
+  -b, --output=VALUE    	 The output file. Specify this or an output
                                directory. Specifying neither writes to the
                                input directory.
+  -o, --output_directory=VALUE         
+							 The output directory. Specify this or an output
+                               file. Specifying neither writes to the input
+                               directory.
   -6, --base64               Encodes the content of the xic vectors as base 64
                                encoded string.
   -s, --stdout               Pipes the output into standard output. Logging is