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NovorAdapter

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

Template for Tool creation

Web Documentation for NovorAdapter

Options

version
Version of the tool that generated this parameters file.
enzyme
Digestion enzyme - currently only Trypsin is supported
fragmentation
Fragmentation method
massAnalyzer
MassAnalyzer e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)
fragment_mass_tolerance
Fragmentation error tolerance (Da)
precursor_mass_tolerance
Precursor error tolerance (ppm or Da)
precursor_error_units
Unit of precursor mass tolerance
variable_modifications
Variable modifications
fixed_modifications
Fixed modifications
forbiddenResidues
Forbidden Resiudes
java_memory
Maximum Java heap size (in MB)
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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novor.jar [,opt.]
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MzML Input file [mzML]
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File to introduce customized algorithm parameters for advanced users (otional .novor file) [novor,opt.]
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The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Java [,opt.]

Output Ports

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Novor idXML output [idXML]

Views

NovorAdapter Std Output
The text sent to standard out during the execution of NovorAdapter.
NovorAdapter Error Output
The text sent to standard error during the execution of NovorAdapter. (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 4.3

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

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Developers

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