IDDecoyProbability

Estimates peptide probabilities using a decoy search strategy.

WARNING: This util is deprecated.

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)
number_of_bins: Number of bins used for the fitting, if sparse datasets are used, this number should be smaller
lower_score_better_default_value_if_zero: This value is used if e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)

: Identification input of combined forward decoy search (reindex with PeptideIndexer first) [idXML,opt.]
: Identification input of forward run [idXML,opt.]
: Identification input of decoy run [idXML,opt.]

: Identification output with forward scores converted to probabilities [idXML]

IDDecoyProbability Std Output: The text sent to standard out during the execution of IDDecoyProbability.
IDDecoyProbability Error Output: The text sent to standard error during the execution of IDDecoyProbability. (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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To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.4

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.2.0.202411141610

On NodePit since: 2024-12-06

Last update: 2024-12-17

KNIME versions: v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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