0 ×

RTPredict

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

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

Web Documentation for RTPredict

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
Overwrite 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)

Input Ports

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

Output Ports

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

Views

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.2
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.