ParquetConverter

Converts between XML and Parquet formats for feature and consensus maps.

potential predecessor tools	→ ParquetConverter →	potential successor tools
Any tool producing featureXML or consensusXML		Any tool consuming featureXML or consensusXML

ParquetConverter converts between XML and Parquet directory formats for FeatureMap and ConsensusMap data. The conversion direction is detected automatically from the input:

• If the input is a featureXML or consensusXML file, the output is a Parquet directory containing multiple .parquet files (features/consensus features, PSMs, proteins, protein groups, search parameters).
• If the input is a Parquet directory (previously exported), the output is a featureXML or consensusXML file.

The command line parameters of this tool are:

ParquetConverter -- Converts between XML and Parquet formats for feature and consensus maps.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_ParquetConverter.html
Version: 3.6.0-pre-nightly-2026-04-01 Apr  2 2026, 01:47:25, Revision: bbb059e
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:
  ParquetConverter <options>

Options (mandatory options marked with '*'):
  -in <path>*        Input file (featureXML, consensusXML) or Parquet directory
  -out <path>*       Output directory (for Parquet export) or file (for XML import)
                     
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.

+ParquetConverterConverts between XML and Parquet formats for feature and consensus maps.

version3.6.0-pre-nightly-2026-04-01 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ParquetConverter'

in Input file (featureXML, consensusXML) or Parquet directoryinput file

out Output directory (for Parquet export) or file (for XML import)output file

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