Groups corresponding features from multiple maps using Wasserstein optimal transport.

potential predecessor tools	→ FeatureLinkerWNet →	potential successor tools
FeatureFinderCentroided (or another feature detection algorithm)		ProteinQuantifier
MapAlignerPoseClustering (or another map alignment algorithm)		TextExporter

This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments using Wasserstein (optimal transport) distance. Features are matched by solving a minimum-cost network flow problem over their (m/z, RT) positions.

For more details and algorithm-specific parameters (set in the ini file) see "Detailed Description" in the algorithm documentation.

FeatureLinkerWNet takes several feature maps (featureXML files) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools.

See also: FeatureLinkerUnlabeledQT FeatureLinkerUnlabeledKD

The command line parameters of this tool are:

FeatureLinkerWNet -- Groups corresponding features from multiple maps using Wasserstein optimal transport.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FeatureLinkerWNet.html
Version: 3.6.0-pre-nightly-2026-06-22 Jun 23 2026, 01:53:23, Revision: 9a7cdde
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:
  FeatureLinkerWNet <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option

Options (mandatory options marked with '*'):
  -in <files>*        Input files separated by blanks (valid formats: 'featureXML', 'consensusXML', 'featurep
                      arquet', 'consensusparquet')
  -out <file>*        Output file (valid formats: 'consensusXML', 'consensusparquet')
  -design <file>      Input file containing the experimental design (valid formats: 'tsv')
                      
  -keep_subelements   For consensusXML/consensusparquet input only: If set, the sub-features of the inputs 
                      are transferred to the output.
                      
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 (0 = all available cores
                      ) (default: '1')
  -write_ini <file>   Writes the default configuration file
  --help              Shows options
  --helphelp          Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/nightly/html/TOPP_FeatureLinkerWNet.html

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.

+FeatureLinkerWNetGroups corresponding features from multiple maps using Wasserstein optimal transport.

version3.6.0-pre-nightly-2026-06-22 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FeatureLinkerWNet'

in[] input files separated by blanksinput file*.featureXML, *.consensusXML, *.featureparquet, *.consensusparquet

out Output fileoutput file*.consensusXML, *.consensusparquet

design input file containing the experimental designinput file*.tsv

keep_subelementsfalse For consensusXML/consensusparquet input only: If set, the sub-features of the inputs are transferred to the output.true, 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 (0 = all available cores)

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

+++algorithmAlgorithm parameters section

distance_metricLINF Distance metric for comparing feature positionsL1, L2, LINF

max_rt_shift100.0 Maximum allowed RT difference (in seconds) for matching features.0.0:∞

mz_unitppm Unit for the m/z tolerance. 'Da' uses max_mz_shift_da; 'ppm' uses max_mz_shift_ppm and log-transforms the m/z axis.Da, ppm

max_mz_shift_da0.3 Maximum allowed m/z difference in Daltons. Used when mz_unit is 'Da'.0.0:∞

max_mz_shift_ppm10.0 Maximum allowed m/z difference in ppm. Used when mz_unit is 'ppm'.0.0:∞

trash_cost0.0 Cost of leaving a feature unmatched (in seconds). Set to 0 to auto-derive from max_rt_shift (a match at the boundary costs the same as no match). Increase to prefer matching over leaving features unmatched.0.0:∞

normalize_intensitiestrue Normalize feature intensities per map before alignment so that total intensity is equal across maps.true, false

decharge_mzfalse Convert observed m/z values to their singly-charged (z=1) equivalent before alignment. Features with charge z>1 are projected to [M+H]+ m/z, making features of the same compound but different charge states directly comparable. If a feature carries a 'dc_charge_adduct_mass' MetaValue (set by MetaboliteFeatureDeconvolution), the stored adduct mass is used; otherwise pure H+ adducts are assumed. Features with unknown charge (z=0) are left unchanged.true, false