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PTPredict

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

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

Web Documentation for PTPredict

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 Ports

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input file [idXML]
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input file with additional model parameters when using the OLIGO kernel [paramXML,opt.]
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input file with the used training dataset when using the OLIGO kernel [txt,opt.]
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svm model in libsvm format (can be produced by PTModel) [txt]

Output Ports

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output file#br# [idXML]

Views

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.2
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