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FeatureLinkerUnlabeled

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

Groups corresponding features from multiple maps.

Web Documentation for FeatureLinkerUnlabeled

Options

version
Version of the tool that generated this parameters file.
keep_subelements
For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.
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)
second_nearest_gap
Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.
use_identifications
Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).
ignore_charge
false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state
ignore_adduct
true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts
max_difference
Never pair features with a larger RT distance (in seconds).
exponent
Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
weight
Final RT distances are weighted by this factor
max_difference
Never pair features with larger m/z distance (unit defined by 'unit')
unit
Unit of the 'max_difference' parameter
exponent
Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
weight
Final m/z distances are weighted by this factor
exponent
Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
weight
Final intensity distances are weighted by this factor
log_transform
Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))

Input Ports

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input files separated by blanks [featureXML,consensusXML]
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input file containing the experimental design [tsv,opt.]

Output Ports

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Output file [consensusXML]

Views

FeatureLinkerUnlabeled Std Output
The text sent to standard out during the execution of FeatureLinkerUnlabeled.
FeatureLinkerUnlabeled Error Output
The text sent to standard error during the execution of FeatureLinkerUnlabeled. (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 4.2

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

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