PTPredict

predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel

Options

version: Version of the tool that generated this parameters file.
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)

: input file [idXML]
: 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 PTModel) [txt]

PTPredict Std Output: The text sent to standard out during the execution of PTPredict.
PTPredict Error Output: The text sent to standard error during the execution of PTPredict. (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: 2024-04-24

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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