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FeatureLinkerLabeled

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Groups corresponding isotope-labeled features in a feature map.

Web Documentation for FeatureLinkerLabeled

Options

version: Version of the tool that generated this parameters file.
log: Name of log file (created only when specified)
debug: Sets the debug level
threads: Sets the number of threads allowed to be used by the TOPP tool
no_progress: Disables progress logging to command line
force: Overrides tool-specific checks
test: Enables the test mode (needed for internal use only)
rt_estimate: If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance.
rt_pair_dist: optimal pair distance in RT [sec] from light to heavy feature
rt_dev_low: maximum allowed deviation below optimal retention time distance
rt_dev_high: maximum allowed deviation above optimal retention time distance
mz_pair_dists: optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)
mz_dev: maximum allowed deviation from optimal m/z distance
mrm: this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)

Input Ports

: Input file [featureXML]

Output Ports

: Output file [consensusXML]

Views

FeatureLinkerLabeled Std Output: The text sent to standard out during the execution of FeatureLinkerLabeled.
FeatureLinkerLabeled Error Output: The text sent to standard error during the execution of FeatureLinkerLabeled. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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