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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="PeakPickerWavelet" description="Finds mass spectrometric peaks in profile mass spectra.">
<ITEM name="version" value="1.11.1" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
<NODE name="1" description="Instance '1' section for 'PeakPickerWavelet'">
<ITEM name="in" value="" type="input-file" description="input profile data file " required="true" advanced="false" supported_formats="*.mzML" />
<ITEM name="out" value="" type="output-file" description="output peak file " required="true" advanced="false" supported_formats="*.mzML" />
<ITEM name="write_peak_meta_data" value="false" type="string" description="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file.Attention: this can blow up files,as 7 arrays are stored per spectrum!" required="false" advanced="true" restrictions="true,false" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="4" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
<NODE name="algorithm" description="Algorithm parameters section">
<ITEM name="signal_to_noise" value="1" type="double" description="Minimal signal to noise ratio for a peak to be picked." required="false" advanced="false" restrictions="0:" />
<ITEM name="centroid_percentage" value="0.8" type="double" description="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." required="false" advanced="true" restrictions="0:1" />
<ITEM name="peak_width" value="0.15" type="double" description="Approximate fwhm of the peaks." required="false" advanced="false" restrictions="0:" />
<ITEM name="estimate_peak_width" value="false" type="string" description="Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored." required="false" advanced="false" restrictions="true,false" />
<ITEM name="fwhm_lower_bound_factor" value="0.7" type="double" description="Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded." required="false" advanced="true" restrictions="0:" />
<ITEM name="fwhm_upper_bound_factor" value="20" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="optimization" value="no" type="string" description="If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional." required="false" advanced="true" restrictions="no,one_dimensional,two_dimensional" />
<NODE name="thresholds" description="">
<ITEM name="peak_bound" value="10" type="double" description="Minimal peak intensity." required="false" advanced="true" restrictions="0:" />
<ITEM name="peak_bound_ms2_level" value="10" type="double" description="Minimal peak intensity for MS/MS peaks." required="false" advanced="true" restrictions="0:" />
<ITEM name="correlation" value="0.5" type="double" description="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." required="false" advanced="true" restrictions="0:1" />
<ITEM name="noise_level" value="0.1" type="double" description="noise level for the search of the peak endpoints." required="false" advanced="true" restrictions="0:" />
<ITEM name="search_radius" value="3" type="int" description="search radius for the search of the maximum in the signal after a maximum in the cwt was found" required="false" advanced="true" restrictions="0:" />
</NODE>
<NODE name="wavelet_transform" description="">
<ITEM name="spacing" value="0.001" type="double" description="spacing of the cwt." required="false" advanced="true" restrictions="0:" />
</NODE>
<NODE name="optimization" description="">
<ITEM name="iterations" value="15" type="int" description="maximal number of iterations for the fitting step" required="false" advanced="true" restrictions="1:" />
<ITEM name="delta_abs_error" value="9.99999974737875e-005" type="double" description="if the absolute error gets smaller than this value the fitting is stopped." required="false" advanced="true" restrictions="0:" />
<ITEM name="delta_rel_error" value="9.99999974737875e-005" type="double" description="if the relative error gets smaller than this value the fitting is stopped" required="false" advanced="true" restrictions="0:" />
<NODE name="penalties" description="">
<ITEM name="position" value="0" type="double" description="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " required="false" advanced="true" restrictions="0:" />
<ITEM name="left_width" value="1" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="right_width" value="1" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="height" value="1" type="double" description="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" />
</NODE>
<NODE name="2d" description="">
<ITEM name="tolerance_mz" value="2.2" type="double" description="mz tolerance for cluster construction" required="false" advanced="true" restrictions="0:" />
<ITEM name="max_peak_distance" value="1.2" type="double" description="maximal peak distance in mz in a cluster" required="false" advanced="true" restrictions="0:" />
</NODE>
</NODE>
<NODE name="deconvolution" description="">
<ITEM name="deconvolution" value="false" type="string" description="If you want heavily overlapping peaks to be separated set this value to "true"" required="false" advanced="true" restrictions="true,false" />
<ITEM name="asym_threshold" value="0.3" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="left_width" value="2" type="double" description="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." required="false" advanced="true" restrictions="0:" />
<ITEM name="right_width" value="2" type="double" description="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." required="false" advanced="true" restrictions="0:" />
<ITEM name="scaling" value="0.12" type="double" description="Initial scaling of the cwt used in the seperation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge." required="false" advanced="true" restrictions="0:" />
<NODE name="fitting" description="">
<ITEM name="fwhm_threshold" value="0.7" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="eps_abs" value="9.99999974737875e-006" type="double" description="if the absolute error gets smaller than this value the fitting is stopped." required="false" advanced="true" restrictions="0:" />
<ITEM name="eps_rel" value="9.99999974737875e-006" type="double" description="if the relative error gets smaller than this value the fitting is stopped." required="false" advanced="true" restrictions="0:" />
<ITEM name="max_iteration" value="10" type="int" description="maximal number of iterations for the fitting step" required="false" advanced="true" restrictions="1:" />
<NODE name="penalties" description="">
<ITEM name="position" value="0" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="height" value="1" type="double" description="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" />
<ITEM name="left_width" value="0" type="double" description="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." required="false" advanced="true" restrictions="0:" />
<ITEM name="right_width" value="0" type="double" description="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." required="false" advanced="true" restrictions="0:" />
</NODE>
</NODE>
</NODE>
<NODE name="SignalToNoiseEstimationParameter" description="">
<ITEM name="max_intensity" value="-1" type="int" description="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)." required="false" advanced="true" restrictions="-1:" />
<ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" required="false" advanced="true" restrictions="0:999" />
<ITEM name="auto_max_percentile" value="95" type="int" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" />
<ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" required="false" advanced="true" restrictions="-1:1" />
<ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="true" restrictions="1:" />
<ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="true" restrictions="3:" />
<ITEM name="stdev_mp" value="3" type="double" description="multiplier for stdev" required="false" advanced="true" restrictions="0.01:999" />
<ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="true" restrictions="1:" />
<ITEM name="noise_for_empty_window" value="1e+020" type="double" description="noise value used for sparse windows" required="false" advanced="true" />
</NODE>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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