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InclusionExclusionListCreator

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Creates inclusion and/or exclusion lists.

Web Documentation for InclusionExclusionListCreator

Options

version
Version of the tool that generated this parameters file.
inclusion_charges
List containing the charge states to be considered for the inclusion list compounds, space separated.
inclusion_strategy
strategy to be used for selection
exclusion_charges
List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated.
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)
missed_cleavages
Number of missed cleavages used for protein digestion.
unit
Create lists with units as seconds instead of minutes
use_relative
Use relative RT window, which depends on RT of precursor.
window_relative
[for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rt*X, rt + rt*X].
window_absolute
[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X].
mz_tol
Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'.
mz_tol_unit
Unit of 'mz_tol'
rt_tol
Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds].
ms2_spectra_per_rt_bin
Number of allowed MS/MS spectra in a retention time bin.
exclude_overlapping_peaks
If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
use_dynamic_exclusion
If true dynamic exclusion is applied.
exclusion_time
The time (in seconds) a feature is excluded.
max_list_size
The maximal number of precursors in the inclusion list.
min_rt
Minimal rt in seconds.
max_rt
Maximal rt in seconds.
rt_step_size
rt step size in seconds.
rt_window_size
rt window size in seconds.
min_protein_id_probability
Minimal protein probability for a protein to be considered identified.
min_pt_weight
Minimal pt weight of a precursor
min_mz
Minimal mz to be considered in protein based LP formulation.
max_mz
Minimal mz to be considered in protein based LP formulation.
use_peptide_rule
Use peptide rule instead of minimal protein id probability
min_peptide_ids
If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
min_peptide_probability
If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified
no_intensity_normalization
Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1.
max_number_precursors_per_feature
The maximal number of precursors per feature.

Input Ports

Inclusion list input file in FASTA or featureXML format. [featureXML,fasta,opt.]
Exclusion list input file in featureXML, idXML or FASTA format. [featureXML,idXML,fasta,opt.]
RTModel file used for the rt prediction of peptides in FASTA files. [txt,opt.]
PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP). [txt,opt.]
File containing the raw data (only needed for FeatureBased_LP). [mzML,opt.]

Output Ports

Output file (tab delimited csv file). [csv]

Views

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

Update Site

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