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    <name>PeakPickerWavelet</name>
    
    <shortDescription>
        Finds mass spectrometric peaks in profile mass spectra.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Finds mass spectrometric peaks in profile mass spectra.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html">Web Documentation for PeakPickerWavelet</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="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!</option>
		<option name="log">Name of log file (created only when specified)</option>
		<option name="debug">Sets the debug level</option>
		<option name="threads">Sets the number of threads allowed to be used by the TOPP tool</option>
		<option name="no_progress">Disables progress logging to command line</option>
		<option name="force">Overwrite tool specific checks.</option>
		<option name="test">Enables the test mode (needed for internal use only)</option>
		<option name="signal_to_noise">Minimal signal to noise ratio for a peak to be picked.</option>
		<option name="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.</option>
		<option name="peak_width">Approximate fwhm of the peaks.</option>
		<option name="estimate_peak_width">Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored.</option>
		<option name="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.</option>
		<option name="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.</option>
		<option name="optimization">If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional.</option>
		<option name="peak_bound">Minimal peak intensity.</option>
		<option name="peak_bound_ms2_level">Minimal peak intensity for MS/MS peaks.</option>
		<option name="correlation">minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped.</option>
		<option name="noise_level">noise level for the search of the peak endpoints.</option>
		<option name="search_radius">search radius for the search of the maximum in the signal after a maximum in the cwt was found</option>
		<option name="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.</option>
		<option name="iterations">maximal number of iterations for the fitting step</option>
		<option name="position">penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized </option>
		<option name="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.</option>
		<option name="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.</option>
		<option name="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.</option>
		<option name="tolerance_mz">mz tolerance for cluster construction</option>
		<option name="max_peak_distance">maximal peak distance in mz in a cluster</option>
		<option name="deconvolution">If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;</option>
		<option name="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.</option>
		<option name="left_width">1/left_width is the initial value for the left width of the peaks found in the deconvolution step.</option>
		<option name="right_width">1/right_width is the initial value for the right width of the peaks found in the deconvolution step.</option>
		<option name="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.</option>
		<option name="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.</option>
		<option name="eps_abs">if the absolute error gets smaller than this value the fitting is stopped.</option>
		<option name="eps_rel">if the relative error gets smaller than this value the fitting is stopped.</option>
		<option name="max_iteration">maximal number of iterations for the fitting step</option>
		<option name="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.</option>
		<option name="height">penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.</option>
		<option name="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.</option>
		<option name="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.</option>
		<option name="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).</option>
		<option name="auto_max_stdev_factor">parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev</option>
		<option name="auto_max_percentile">parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile</option>
		<option name="auto_mode">method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method</option>
		<option name="win_len">window length in Thomson</option>
		<option name="bin_count">number of bins for intensity values</option>
		<option name="stdev_mp">multiplier for stdev</option>
		<option name="min_required_elements">minimum number of elements required in a window (otherwise it is considered sparse)</option>
		<option name="noise_for_empty_window">noise value used for sparse windows</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzML]">input profile data file  [mzML]</inPort>
		<outPort index="0" name="out [mzML]">output peak file  [mzML]</outPort>
 </ports>
    <views>
        <view index="0" name="PeakPickerWavelet Std Output">The text sent to standard out during the execution of PeakPickerWavelet.</view>
        <view index="1" name="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.)</view>
    </views>    
</knimeNode>
