IDMerger

Merges several protein/peptide identification files into one file.

Options

version: Version of the tool that generated this parameters file.
annotate_file_origin: Store the original filename in each protein/peptide identification (meta value: 'file_origin') - idXML input/output only
pepxml_protxml: Merge idXML files derived from a pepXML and corresponding protXML file. Exactly two input files are expected in this case. Not compatible with 'add_to'.
merge_proteins_add_PSMs: Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s. Not compatible with 'add_to'.
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 files separated by blanks (all must have the same type) [idXML,oms]
: Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum). [idXML,opt.]

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

v5.4

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: 3.2.0.202411141610

On NodePit since: 2024-12-06

Last update: 2024-12-30

KNIME versions: v5.4, v5.3, 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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