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:

INIUpdater -- Update INI and TOPPAS files to new OpenMS version.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_INIUpdater.html
Version: 3.6.0-pre-nightly-2026-03-27 Mar 28 2026, 01:46:35, Revision: cb6c7d1
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry 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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+INIUpdaterUpdate INI and TOPPAS files to new OpenMS version.

version3.6.0-pre-nightly-2026-03-27 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