RTPredict

Predicts retention times for peptides using a model trained by RTModel.

Options

version: Version of the tool that generated this parameters file.
total_gradient_time: The time (in seconds) of the gradient (peptide RT prediction)
max_number_of_peptides: The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory).
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)
rewrite_peptideidentification_rtmz: Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)

: Peptides with precursor information [idXML,opt.]
: Peptides as text-based file [txt,opt.]
: input file with additional model parameters when using the OLIGO kernel [paramXML,opt.]
: input file with the used training dataset when using the OLIGO kernel [txt,opt.]
: svm model in libsvm format (can be produced by RTModel) [txt]

: Output file with peptide RT prediction [idXML]
: Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well. [idXML]
: Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well. [idXML]
: Output file with predicted RT values [csv]

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

v5.2

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: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-04-18

KNIME versions: 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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