IconPeakPickerWavelet0 ×

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

Finds mass spectrometric peaks in profile mass spectra.

Web Documentation for PeakPickerWavelet

Options

version
Version of the tool that generated this parameters file.
write_peak_meta_data
Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file. Attention: this can blow up files, since seven arrays are stored per spectrum!
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)
signal_to_noise
Minimal signal to noise ratio for a peak to be picked.
centroid_percentage
Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity.
peak_width
Approximate fwhm of the peaks.
estimate_peak_width
Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored.
fwhm_lower_bound_factor
Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded.
fwhm_upper_bound_factor
Factor that calculates the maximal fwhm value from the peak_width. All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded.
optimization
If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional.
peak_bound
Minimal peak intensity.
peak_bound_ms2_level
Minimal peak intensity for MS/MS peaks.
correlation
minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped.
noise_level
noise level for the search of the peak endpoints.
search_radius
search radius for the search of the maximum in the signal after a maximum in the cwt was found
spacing
Spacing of the CWT. Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most.
iterations
maximal number of iterations for the fitting step
position
penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized
left_width
penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized.
right_width
penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized.
height
penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized.
tolerance_mz
mz tolerance for cluster construction
max_peak_distance
maximal peak distance in mz in a cluster
deconvolution
If you want heavily overlapping peaks to be separated set this value to "true"
asym_threshold
If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started.
left_width
1/left_width is the initial value for the left width of the peaks found in the deconvolution step.
right_width
1/right_width is the initial value for the right width of the peaks found in the deconvolution step.
scaling
Initial scaling of the cwt used in the separation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge.
fwhm_threshold
If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started.
eps_abs
if the absolute error gets smaller than this value the fitting is stopped.
eps_rel
if the relative error gets smaller than this value the fitting is stopped.
max_iteration
maximal number of iterations for the fitting step
position
penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule.
height
penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.
left_width
penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.
right_width
penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.
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 not be added to the histogram. 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).
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
stdev_mp
multiplier for stdev
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

Input Ports

input profile data file [mzML]

Output Ports

output peak file [mzML]

Views

PeakPickerWavelet Std Output
The text sent to standard out during the execution of PeakPickerWavelet.
PeakPickerWavelet Error Output
The text sent to standard error during the execution of PeakPickerWavelet. (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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