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ProteinResolver

protein inference

Web Documentation for ProteinResolver

Options

version: Version of the tool that generated this parameters file.
in_path: Path to idXMLs or consensusXMLs files. Ignored if 'in' is given.
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)
missed_cleavages: Number of allowed missed cleavages
min_length: Minimum length of peptide
enzyme: Digestion enzyme
experiment: Identifier for the experimental design.
file: Identifier for the file name.
separator: Separator, which should be used to split a row into columns

Input Ports

: Input database file [fasta]
: Input file(s) holding experimental data [idXML,consensusXML,opt.]
: Text file containing the experimental design. See documentation for specific format requirements [txt,opt.]

Output Ports

: output file. Contains all protein groups [csv]
: output file. Contains one peptide per line and all proteins which contain that peptide [csv]
: output file. Contains one protein per line [csv]
: output file for additional info [csv]

Popular Predecessors

Popular Successors

Views

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

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: 2024-11-20

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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