QualityControl

Computes various QC metrics.

Many input formats are supported only the consensusXML is required.

The more optional files you provide, the more metrics you get.

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).

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

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.)

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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:

v5.3

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: 3.2.0.202409181756

On NodePit since: 2024-10-17

Last update: 2024-11-21

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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