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OpenSwathDecoyGenerator

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

Generates decoys according to different models for a specific TraML

Web Documentation for OpenSwathDecoyGenerator

Options

version
Version of the tool that generated this parameters file.
in_type
Input file type -- default: determined from file extension or content
out_type
Output file type -- default: determined from file extension or content
method
decoy generation method ('shuffle','pseudo-reverse','reverse','shift')
decoy_tag
decoy tag
min_decoy_fraction
Minimum fraction of decoy / target peptides and proteins
aim_decoy_fraction
Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)
shuffle_max_attempts
shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm
shuffle_sequence_identity_threshold
shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm
shift_precursor_mz_shift
shift: precursor ion MZ shift in Thomson for shift decoy method
shift_product_mz_shift
shift: fragment ion MZ shift in Thomson for shift decoy method
product_mz_threshold
MZ threshold in Thomson for fragment ion annotation
allowed_fragment_types
allowed fragment types
allowed_fragment_charges
allowed fragment charge states
enable_detection_specific_losses
set this flag if specific neutral losses for detection fragment ions should be allowed
enable_detection_unspecific_losses
set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed
switchKR
Whether to switch terminal K and R (to achieve different precursor mass)
separate
set this flag if decoys should not be appended to targets.
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 [tsv,mrm,pqp,TraML]

Output Ports

Output file [tsv,pqp,TraML]

Views

OpenSwathDecoyGenerator Std Output
The text sent to standard out during the execution of OpenSwathDecoyGenerator.
OpenSwathDecoyGenerator Error Output
The text sent to standard error during the execution of OpenSwathDecoyGenerator. (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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Update Site

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

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