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PSMFeatureExtractor

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Computes extra features for each input PSM.

Web Documentation for PSMFeatureExtractor

Options

version
Version of the tool that generated this parameters file.
extra
List of the MetaData parameters to be included in a feature set for precolator.
multiple_search_engines
Combine PSMs from different search engines by merging on scan level.
skip_db_check
Manual override to skip the check if same settings for multiple search engines were applied. Only valid together with -multiple_search_engines flag.
concat
Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level. Only valid together with -multiple_search_engines flag.
impute
Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed. Only valid together with -multiple_search_engines flag.
limit_imputation
Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score. Only valid together with -multiple_search_engines flag.
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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)

Input Ports

Input file(s) [mzid,idXML]

Output Ports

Output file in mzid or idXML format [mzid,idXML]

Views

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

Installation

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

KNIME 3.7
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