PeakPickerHiRes

Options

version

Version of the tool that generated this parameters file.

processOption

Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first

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)

signal_to_noise

Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)

spacing_difference_gap

The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.

spacing_difference

Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.

missing

Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.

ms_levels

List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes.

report_FWHM

Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.

report_FWHM_unit

Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).

max_intensity

maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.

auto_max_stdev_factor

parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev

auto_max_percentile

parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile

auto_mode

method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method

win_len

window length in Thomson

bin_count

number of bins for intensity values

min_required_elements

minimum number of elements required in a window (otherwise it is considered sparse)

noise_for_empty_window

noise value used for sparse windows

write_log_messages

Write out log messages in case of sparse windows or median in rightmost histogram bin

Views

PeakPickerHiRes Std Output

The text sent to standard out during the execution of PeakPickerHiRes.

PeakPickerHiRes Error Output

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

Workflows

• Calculate_variable_DIA_windowsKNIME Hub

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