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DatabaseFilter

Filters a protein database (FASTA format) based on identified proteins

Web Documentation for DatabaseFilter

Options

version: Version of the tool that generated this parameters file.
method: Switch between white-/blacklisting
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 FASTA file, containing a database. [fasta]
: Input file containing identified peptides and proteins. [idXML,mzid]

Output Ports

: Output FASTA file where the reduced database will be written to. [fasta]

Popular Predecessors

Popular Successors

Port to URI100 %

Views

DatabaseFilter Std Output: The text sent to standard out during the execution of DatabaseFilter.
DatabaseFilter Error Output: The text sent to standard error during the execution of DatabaseFilter. (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: 2024-07-22

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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