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PercolatorAdapter

Facilitate input to Percolator and reintegrate.

Web Documentation for PercolatorAdapter

Options

version: Version of the tool that generated this parameters file.
enzyme: Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp
peptide_level_fdrs: Calculate peptide-level FDRs instead of PSM-level FDRs.
protein_level_fdrs: Use the picked protein-level FDR to infer protein probabilities. Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern.
osw_level: OSW: the data level selected for scoring.
score_type: Type of the peptide main score
generic_feature_set: Use only generic (i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly.
subset_max_train: Only train an SVM on a subset of <x> PSMs, and use the resulting score vector to evaluate the other PSMs. Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal.
cpos: Cpos, penalty for mistakes made on positive examples. Set by cross validation if not specified.
cneg: Cneg, penalty for mistakes made on negative examples. Set by cross validation if not specified.
testFDR: False discovery rate threshold for evaluating best cross validation result and the reported end result.
trainFDR: False discovery rate threshold to define positive examples in training. Set to testFDR if 0.
maxiter: Maximal number of iterations
nested_xval_bins: Number of nested cross-validation bins in the 3 splits.
quick_validation: Quicker execution by reduced internal cross-validation.
static: Use static model (requires init-weights parameter to be set)
default_direction: The most informative feature given as the feature name, can be negated to indicate that a lower value is better.
verbose: Set verbosity of output: 0=no processing info, 5=all.
unitnorm: Use unit normalization [0-1] instead of standard deviation normalization
test_each_iteration: Measure performance on test set each iteration
override: Override error check and do not fall back on default score vector in case of suspect score vector
seed: Setting seed of the random number generator.
doc: Include description of correct features
klammer: Retention time features calculated as in Klammer et al. Only available if -doc is set
decoy_pattern: Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active).
post_processing_tdc: Use target-decoy competition to assign q-values and PEPs.
train_best_positive: Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration. If the user only provides one PSM per spectrum, this filter will have no effect.
ipf_max_peakgroup_pep: OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability.
ipf_max_transition_isotope_overlap: OSW/IPF: Maximum isotope overlap to consider transitions in IPF.
ipf_min_transition_sn: OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF. Set -1 to disable this filter.
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 file(s) [mzid,idXML,opt.]
: Input decoy file(s) in case of separate searches [mzid,idXML,opt.]
: Input file in OSW format [OSW,opt.]
: Read initial weights to the given file [tsv,opt.]
: Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active). [FASTA,opt.]

Output Ports

: Output file [idXML,mzid,osw]
: Write pin file (e.g., for debugging) [tsv]
: Write pout file (e.g., for debugging) [tab]
: Write pout file (e.g., for debugging) [tab]
: Write pout file (e.g., for debugging) [tab]
: Write pout file (e.g., for debugging) [tab]
: Output final weights to the given file [tsv]

Views

PercolatorAdapter Std Output: The text sent to standard out during the execution of PercolatorAdapter.
PercolatorAdapter Error Output: The text sent to standard error during the execution of PercolatorAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Plugin version: 2.7.0.202109131426

On NodePit since: 2022-12-06

Last update: 2024-11-09

KNIME versions: From v3.6 to v4.7

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