INIUpdater

Update INI and TOPPAS files from previous versions of OpenMS/TOPP

This tool can update old INI files and make them

• compatible to new versions of OpenMS
• show new parameters introduced with a new OpenMS version
• delete old parameters which no longer have any effect

The new INI files can be created in-place (with -i option), which will overwrite the existing file, but create a backup copy with [filename]_[version].ini, e.g.

INIUpdater -in FileFilter.ini -i

will create a file FileFilter_1.8.ini if the old ini version was 1.8.

No backup will be created if -out is used, as the original files are not touched (unless you name them the same).

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

INIUpdater -- Update INI and TOPPAS files to new OpenMS version.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_INIUpdater.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  INIUpdater <options>

Options (mandatory options marked with '*'):
  -in <files>*       INI/TOPPAS files that need updating. (valid formats: 'ini', 'toppas')
  -i                 In-place: Override given INI/TOPPAS files with new content (not compatible with -out)
  -out <files>       Optional list of output files (not compatible with -i). (valid formats: 'ini', 'toppas')
                     
Common TOPP options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+INIUpdaterUpdate INI and TOPPAS files to new OpenMS version.

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'INIUpdater'

in[] INI/TOPPAS files that need updating.input file*.ini, *.toppas

ifalse in-place: Override given INI/TOPPAS files with new content (not compatible with -out)true, false

out[] Optional list of output files (not compatible with -i).output file*.ini, *.toppas

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false