QualityControl

Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.

Web Documentation for QualityControl

Options

version
Version of the tool that generated this parameters file.
out_evd
If a Path is given, a MQEvidence txt-file will be created in this directory. If the directory does not exist, it will be created as well.
out_msms
If a Path is given, a MQMsms txt-file will be created in this directory. If the directory does not exist, it will be created as well.
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)
unit
Unit for mass tolerance. 'auto' uses information from FeatureXML
tolerance
m/z search window for matching peaks in two spectra
assume_all_target
Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits).

Input Ports

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ConsensusXML input, generated by FeatureLinker. [consensusXML]
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MzML input (after InternalCalibration, if available) [mzML,opt.]
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FeatureXMLs after FDR filtering [featureXML,opt.]
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Proteins considered contaminants [fasta,opt.]
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FASTA file used during MS/MS identification (including decoys). If the protein description contains 'GN=...' then gene names will be extracted [fasta,opt.]
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trafoXMLs from MapAligners [trafoXML,opt.]

Output Ports

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Output mzTab with QC information [mzTab]
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ConsensusXML with QC information (as metavalues) [consensusXML]
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FeatureXMLs with QC information (as metavalues) [featureXML]

Popular Predecessors

Popular Successors

Views

QualityControl Std Output
The text sent to standard out during the execution of QualityControl.
QualityControl Error Output
The text sent to standard error during the execution of QualityControl. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Links

Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

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: 3.0.0.202307112039
On NodePit since: 2023-12-06
Last update: 2024-04-19
KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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