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QualityControl

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

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.
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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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]

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.)

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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