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MaRaClusterAdapter

Facilitate input to MaRaCluster and reintegrate.

Web Documentation for MaRaClusterAdapter

Options

version: Version of the tool that generated this parameters file.
output_directory: Output directory for MaRaCluster original consensus output
pcut: log(p-value) cutoff, has to be < 0.0. Default: -10.0.
min_cluster_size: minimum number of spectra in a cluster for consensus spectra
verbose: Set verbosity of output: 0=no processing info, 5=all.
precursor_tolerance: Precursor monoisotopic mass tolerance
precursor_tolerance_units: tolerance_mass_units 0=ppm, 1=Da
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

: Input file(s) [mzML,mgf]
: Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation [idXML,opt.]

Output Ports

: Output file in idXML format [idXML]
: Consensus spectra in mzML format [mzML]

Popular Predecessors

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Popular Successors

Views

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

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Plugin version: 2.7.0.202109131426

On NodePit since: 2022-12-06

Last update: 2024-04-13

KNIME versions: From v3.6 to v4.7

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