Update README.md

Author: nielshulstaert

README.md

@@ -2,7 +2,7 @@
 
 Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too). It takes a thermo RAW file as input and outputs a metadata file and the spectra in 3 possible formats
 * MGF: only MS2 spectra
-* mzML: both MS1 and MS2 spectra
+* mzML and indexed mzML: both MS1 and MS2 spectra
 * Apache Parquet: under development
 
 RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved
@@ -12,44 +12,34 @@ RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc.
 
 ## Usage
 ```
-mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0 -c=PXD00001
+mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0
 ```
-For running on Windows, omit `mono`. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata `-m=0|1` (0 for JSON format, 1 for TXT format) and the spectra file `-f` or both. For the MGF format, `-p` flag is used to exclude MS2 profile mode data (the MGF files can get big when the MS2 spectra were acquired in profile mode). 
+For running on Windows, omit `mono`. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata `-m=0|1` (0 for MGF, 1 for mzMl, 2 for indexed mzML, 3 for Parquet, 4 for MGF with profile data excluded) and the spectra file `-f` or both. The 'MGF with profile data excluded format' is used to exclude MS2 profile mode data (the MGF files can get big when the MS2 spectra were acquired in profile mode). 
 
 ```
-ThermoRawFileParser.exe usage is (use -option=value for the optional arguments):
+ThermoRawFileParser.exe  usage is (use -option=value for the optional arguments):
   -h, --help                 Prints out the options.
   -i, --input=VALUE          The raw file input.
   -o, --output=VALUE         The output directory.
   -f, --format=VALUE         The output format for the spectra (0 for MGF, 1
-                               for MzMl, 2 for Parquet)
+                               for mzMl, 2 for indexed mzML, 3 for Parquet, 4
+                               for MGF with profile data excluded)
   -m, --metadata=VALUE       The metadata output format (0 for JSON, 1 for TXT).
   -g, --gzip                 GZip the output file if this flag is specified (
                                without value).
-  -p, --profiledata          Exclude MS2 profile data if this flag is specified
-                               (without value). Only for MGF format!
-  -c, --collection[=VALUE]   The optional collection identifier (PXD identifier
-                               for example).
-  -r, --run[=VALUE]          The optional mass spectrometry run name used in
-                               the spectrum title. The RAW file name will be
-                               used if not specified.
-  -s, --subfolder[=VALUE]    Optional, to disambiguate instances where the same
-                               collection has 2 or more MS runs with the same
-                               name.
   -u, --s3_url[=VALUE]       Optional property to write directly the data into
-                               S3 Storage
+                               S3 Storage.
   -k, --s3_accesskeyid[=VALUE]
                              Optional key for the S3 bucket to write the file
-                               output
+                               output.
   -t, --s3_secretaccesskey[=VALUE]
                              Optional key for the S3 bucket to write the file
-                               output
+                               output.
   -n, --s3_bucketName[=VALUE]
                              S3 bucket name
-  -v, --verbose              Verbose the programm and the individual steps
+  -v, --verbose              Enable verbose logging.
   -e, --ignoreInstrumentErrors
                              Ignore missing properties by the instrument.
-
 ```
 
 ## Download
@@ -74,14 +64,14 @@ docker build --no-cache -t thermorawparser -f Dockerfile_basic .
 ```
 Run example:
 ```
-docker run -v /home/user/raw:/data_input -i -t thermorawparser mono /src/bin/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
+docker run -v /home/user/raw:/data_input -i -t thermorawparser mono /src/bin/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
 ```
 Create example for reusing the container:
 ```
 docker create -v /home/user/raw:/data_input --name=rawparser -it thermorawparser
 docker start rawparser
-docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
-docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/another_raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
+docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
+docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/another_raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
 docker stop rawparser
 ```
 
@@ -93,9 +83,9 @@ docker build --no-cache -t thermorawparser .
 ```
 Run example:
 ```
-docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser mono /home/biodocker/bin/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
+docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser mono /home/biodocker/bin/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
 ```
 or with the bash script (`ThermoRawFileParser.sh`):
 ```
-docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser /bin/bash /home/biodocker/bin/ThermoRawFileParser.sh -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0 -c=PXD00001
+docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser /bin/bash /home/biodocker/bin/ThermoRawFileParser.sh -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
 ```