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

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

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.)

Workflows

• basic_peptide_identificationKNIME Hub
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTKNIME Hub
• MHCquantKNIME Hub
• Peptide Identification from MSKNIME Hub
• Show all 13 workflows

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Developers