TargetedFileConverter

Converts different transition files for targeted proteomics / metabolomics analysis.

Options

version: Version of the tool that generated this parameters file.
in_type: input file type -- default: determined from file extension or content
legacy_traml_id: PQP to TraML: Should legacy TraML IDs be used?
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)
retentionTimeInterpretation: How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)
override_group_label_check: Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing.
force_invalid_mods: Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)

: Input file to convert.#br# See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file. [tsv,mrm,pqp,TraML]

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

v5.2

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, v3.7, v3.6

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