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PercolatorAdapter

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

Facilitate input to Percolator and reintegrate.

Web Documentation for PercolatorAdapter

Options

version
Version of the tool that generated this parameters file.
out_type
Output file type -- default: determined from file extension or content.
enzyme
Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin
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: Either "ms1", "ms2" or "transition"; 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
quick-validation
Quicker execution by reduced internal cross-validation.
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
Overwrite 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 [,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 [mzid,idXML,osw]
Write pin file (e.g., for debugging) [tab,Inactive]
Output final weights to the given file [Inactive]

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.)

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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