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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="PeakPicker" description="">
    <NODE name="1" description="Instance '1' section for 'PeakPicker'">
      <ITEM name="in" value="" type="string" description="input profile data file (valid formats: 'mzData')" tags="input file" />
      <ITEM name="out" value="" type="string" description="output peak file (valid formats: 'mzData')" tags="output file" />
      <ITEM name="type" value="wavelet" type="string" description="peak detection algorithm type" restrictions="wavelet,high_res" />
      <ITEM name="log" value="TOPP.log" type="string" description="Location of the log file" tags="advanced" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" restrictions="true,false" />
      <NODE name="algorithm" description="Algorithm parameters section">
        <ITEM name="signal_to_noise" value="3" type="float" description="Minimal signal to noise ratio for a peak to be picked." restrictions="0:" />
        <ITEM name="centroid_percentage" value="0.8" type="float" 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." tags="advanced" restrictions="0:1" />
        <ITEM name="peak_width" value="0.2" type="float" description="Approximate fwhm of the peaks." 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." restrictions="true,false" />
        <ITEM name="fwhm_bound_factor" value="0.7" type="float" description="Factor that calculates the minimal fwhm value from the peak_width." tags="advanced" 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." tags="advanced" restrictions="no,one_dimensional,two_dimensional" />
        <ITEM name="signal_to_noise" value="4" type="float" description="Minimal signal to noise ratio for a peak to be picked." restrictions="0:" />
        <ITEM name="centroid_percentage" value="0.8" type="float" 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." tags="advanced" restrictions="0:1" />
        <ITEM name="peak_width" value="0.2" type="float" description="Approximate fwhm of the peaks." 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." restrictions="true,false" />
        <ITEM name="fwhm_bound_factor" value="0.7" type="float" description="Factor that calculates the minimal fwhm value from the peak_width." tags="advanced" 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." tags="advanced" restrictions="no,one_dimensional,two_dimensional" />
        <NODE name="thresholds" description="">
          <ITEM name="peak_bound" value="10" type="float" description="Minimal peak intensity." tags="advanced" restrictions="0:" />
          <ITEM name="peak_bound_ms2_level" value="10" type="float" description="Minimal peak intensity for MS/MS peaks." tags="advanced" restrictions="0:" />
          <ITEM name="correlation" value="0.5" type="float" description="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." tags="advanced" restrictions="0:1" />
          <ITEM name="noise_level" value="0.1" type="float" description="noise level for the search of the peak endpoints." tags="advanced" 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" tags="advanced" restrictions="0:" />
        </NODE>
        <NODE name="wavelet_transform" description="">
          <ITEM name="spacing" value="0.001" type="float" description="spacing of the cwt." tags="advanced" restrictions="0:" />
        </NODE>
        <NODE name="optimization" description="">
          <ITEM name="iterations" value="15" type="int" description="maximal number of iterations for the fitting step" tags="advanced" restrictions="1:" />
          <NODE name="penalties" description="">
            <ITEM name="position" value="0" type="float" description="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " tags="advanced" restrictions="0:" />
            <ITEM name="left_width" value="1" type="float" 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." tags="advanced" restrictions="0:" />
            <ITEM name="right_width" value="1" type="float" 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." tags="advanced" restrictions="0:" />
            <ITEM name="height" value="1" type="float" 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." tags="advanced" restrictions="0:" />
          </NODE>
          <NODE name="2d" description="">
            <ITEM name="tolerance_mz" value="2.2" type="float" description="mz tolerance for cluster construction" tags="advanced" restrictions="0:" />
            <ITEM name="max_peak_distance" value="1.2" type="float" description="maximal peak distance in mz in a cluster" tags="advanced" 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'" tags="advanced" restrictions="true,false" />
          <ITEM name="asym_threshold" value="0.3" type="float" 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." tags="advanced" restrictions="0:" />
          <ITEM name="left_width" value="2" type="float" description="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." tags="advanced" restrictions="0:" />
          <ITEM name="right_width" value="2" type="float" description="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." tags="advanced" restrictions="0:" />
          <ITEM name="scaling" value="0.12" type="float" 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." tags="advanced" restrictions="0:" />
          <NODE name="fitting" description="">
            <ITEM name="fwhm_threshold" value="0.7" type="float" 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." tags="advanced" restrictions="0:" />
            <ITEM name="eps_abs" value="9.99999974737875e-006" type="float" description="if the absolute error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" />
            <ITEM name="eps_rel" value="9.99999974737875e-006" type="float" description="if the relative error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" />
            <ITEM name="max_iteration" value="10" type="int" description="maximal number of iterations for the fitting step" tags="advanced" restrictions="1:" />
            <NODE name="penalties" description="">
              <ITEM name="position" value="0" type="float" 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." tags="advanced" restrictions="0:" />
              <ITEM name="height" value="1" type="float" description="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." tags="advanced" restrictions="0:" />
              <ITEM name="left_width" value="0" type="float" 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." tags="advanced" restrictions="0:" />
              <ITEM name="right_width" value="0" type="float" 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." tags="advanced" 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)." tags="advanced" restrictions="-1:" />
          <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" restrictions="0:100" />
          <ITEM name="auto_mode" value="0" type="int" description="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" tags="advanced" restrictions="-1:1" />
          <ITEM name="win_len" value="200" type="float" description="window length in Thomson" tags="advanced" restrictions="1:" />
          <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" tags="advanced" restrictions="3:" />
          <ITEM name="stdev_mp" value="3" type="float" description="multiplier for stdev" tags="advanced" 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)" tags="advanced" restrictions="1:" />
          <ITEM name="noise_for_empty_window" value="1e+020" type="float" description="noise value used for sparse windows" tags="advanced" />
        </NODE>
        <NODE name="thresholds" description="">
          <ITEM name="peak_bound" value="10" type="float" description="Minimal peak intensity." tags="advanced" restrictions="0:" />
          <ITEM name="peak_bound_ms2_level" value="10" type="float" description="Minimal peak intensity for MS/MS peaks." tags="advanced" restrictions="0:" />
          <ITEM name="correlation" value="0.5" type="float" description="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." tags="advanced" restrictions="0:1" />
          <ITEM name="noise_level" value="0.1" type="float" description="noise level for the search of the peak endpoints." tags="advanced" 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" tags="advanced" restrictions="0:" />
        </NODE>
        <NODE name="wavelet_transform" description="">
          <ITEM name="spacing" value="0.001" type="float" description="spacing of the cwt." tags="advanced" restrictions="0:" />
        </NODE>
        <NODE name="optimization" description="">
          <ITEM name="iterations" value="15" type="int" description="maximal number of iterations for the fitting step" tags="advanced" restrictions="1:" />
          <NODE name="penalties" description="">
            <ITEM name="position" value="0" type="float" description="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " tags="advanced" restrictions="0:" />
            <ITEM name="left_width" value="1" type="float" 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." tags="advanced" restrictions="0:" />
            <ITEM name="right_width" value="1" type="float" 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." tags="advanced" restrictions="0:" />
            <ITEM name="height" value="1" type="float" 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." tags="advanced" restrictions="0:" />
          </NODE>
          <NODE name="2d" description="">
            <ITEM name="tolerance_mz" value="2.2" type="float" description="mz tolerance for cluster construction" tags="advanced" restrictions="0:" />
            <ITEM name="max_peak_distance" value="1.2" type="float" description="maximal peak distance in mz in a cluster" tags="advanced" 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'" tags="advanced" restrictions="true,false" />
          <ITEM name="asym_threshold" value="0.3" type="float" 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." tags="advanced" restrictions="0:" />
          <ITEM name="left_width" value="2" type="float" description="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." tags="advanced" restrictions="0:" />
          <ITEM name="right_width" value="2" type="float" description="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." tags="advanced" restrictions="0:" />
          <ITEM name="scaling" value="0.12" type="float" 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." tags="advanced" restrictions="0:" />
          <NODE name="fitting" description="">
            <ITEM name="fwhm_threshold" value="0.7" type="float" 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." tags="advanced" restrictions="0:" />
            <ITEM name="eps_abs" value="9.99999974737875e-006" type="float" description="if the absolute error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" />
            <ITEM name="eps_rel" value="9.99999974737875e-006" type="float" description="if the relative error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" />
            <ITEM name="max_iteration" value="10" type="int" description="maximal number of iterations for the fitting step" tags="advanced" restrictions="1:" />
            <NODE name="penalties" description="">
              <ITEM name="position" value="0" type="float" 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." tags="advanced" restrictions="0:" />
              <ITEM name="height" value="1" type="float" description="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." tags="advanced" restrictions="0:" />
              <ITEM name="left_width" value="0" type="float" 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." tags="advanced" restrictions="0:" />
              <ITEM name="right_width" value="0" type="float" 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." tags="advanced" 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)." tags="advanced" restrictions="-1:" />
          <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" restrictions="0:100" />
          <ITEM name="auto_mode" value="0" type="int" description="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" tags="advanced" restrictions="-1:1" />
          <ITEM name="win_len" value="200" type="float" description="window length in Thomson" tags="advanced" restrictions="1:" />
          <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" tags="advanced" restrictions="3:" />
          <ITEM name="stdev_mp" value="3" type="float" description="multiplier for stdev" tags="advanced" 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)" tags="advanced" restrictions="1:" />
          <ITEM name="noise_for_empty_window" value="1e+020" type="float" description="noise value used for sparse windows" tags="advanced" />
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>