MapStatistics

Extract extended statistics on the features of a map for quality control.

pot. predecessor tools	→ MapStatistics →	pot. successor tools
FeatureFinder, FeatureMatcher		-

This tool computes some basic statistics on the features of a map that are frequently used for quality control.

Information displayed includes:

• show information about the data range of a file (m/z, RT, intensity)
• show a statistical summary for intensities, qualities, feature widths
• break down the statistics for fractions of the map
• total ion current included in the features as a function of RT

The command line parameters of this tool are:

MapStatistics -- Extract extended statistics on the features of a map for quality control.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MapStatistics.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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:
  MapStatistics <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file (valid formats: 'featureXML', 'consensusXML')
  -in_type <type>    Input file type -- default: determined from file extension or content (valid: 'featureXM
                     L', 'consensusXML')
  -out <file>        Optional output txt file. If empty, the output is written to the command line. (valid 
                     formats: 'txt')
  -n <n>             Report separate statistics for each of n RT slices of the map. (default: '4') (min: '1' 
                     max: '100')
  -m                 Show meta information about the whole experiment
  -p                 Shows data processing information
  -s                 Computes a summary statistics of intensities, qualities, and widths
                     
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.

+MapStatisticsExtract extended statistics on the features of a map for quality control.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MapStatistics'

in Input fileinput file*.featureXML, *.consensusXML

in_type Input file type -- default: determined from file extension or contentfeatureXML, consensusXML

out Optional output txt file. If empty, the output is written to the command line.output file*.txt

n4 Report separate statistics for each of n RT slices of the map.1:100

mfalse Show meta information about the whole experimenttrue, false

pfalse Shows data processing informationtrue, false

sfalse Computes a summary statistics of intensities, qualities, and widthstrue, false

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