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

Overrides 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.

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.)

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