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QCCalculator

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

Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.

Web Documentation for QCCalculator

Options

version
Version of the tool that generated this parameters file.
remove_duplicate_features
This flag should be set, if you work with a set of merged features.
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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raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information) [mzML]
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Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read format [idXML,opt.]
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feature input file (this is relevant for most QC issues) [featureXML,opt.]
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consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger) [consensusXML,opt.]

Output Ports

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Your qcML file. [qcML]

Views

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

Workflows

Installation

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

KNIME 4.2
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Developers

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