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TargetedFileConverter

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

Converts different transition files for targeted proteomics / metabolomics analysis.

Web Documentation for TargetedFileConverter

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 Ports

Icon
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]

Output Ports

Icon
Output file [tsv,pqp,TraML]

Views

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2

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

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Developers

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