QCCalculator

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

Options

version: Version of the tool that generated this parameters file.
label: unique name for the run that can be used in a figure label
name: name of the person creating this mzQC file
address: contact address (mail/e-mail or phone)
description: description and comments about the mzQC file contents
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)

: raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information) [mzML]
: Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read format [idXML,opt.]
: feature input file (this is relevant for most QC issues) [featureXML,opt.]
: consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger) [consensusXML,opt.]

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.)

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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:

v5.4

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: 3.2.0.202411141610

On NodePit since: 2024-12-06

Last update: 2024-12-21

KNIME versions: v5.4, v5.3, 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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