view TOFCalibration.xml @ 1:17e8c91b70d5 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="TOFCalibration" name="TOFCalibration" version="1.12.0">
  <description>Applies time of flight calibration.</description>
  <macros>
    <token name="@EXECUTABLE@">TOFCalibration</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>TOFCalibration

-in ${param_in}
-out ${param_out}
-ext_calibrants ${param_ext_calibrants}
-ref_masses ${param_ref_masses}
-tof_const ${param_tof_const}
${param_peak_data}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:PeakPicker:signal_to_noise ${param_signal_to_noise}
-algorithm:PeakPicker:peak_width ${param_peak_width}
${param_estimate_peak_width}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:PeakPicker:centroid_percentage ${adv_opts.param_centroid_percentage}
    -algorithm:PeakPicker:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor}
    -algorithm:PeakPicker:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor}
    -algorithm:PeakPicker:optimization:iterations ${adv_opts.param_iterations}
    -algorithm:PeakPicker:optimization:penalties:position ${adv_opts.param_position}
    -algorithm:PeakPicker:optimization:penalties:left_width ${adv_opts.param_left_width}
    -algorithm:PeakPicker:optimization:penalties:right_width ${adv_opts.param_right_width}
    -algorithm:PeakPicker:optimization:penalties:height ${adv_opts.param_height}
    -algorithm:PeakPicker:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz}
    -algorithm:PeakPicker:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance}
    -algorithm:PeakPicker:thresholds:peak_bound ${adv_opts.param_peak_bound}
    -algorithm:PeakPicker:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level}
    -algorithm:PeakPicker:thresholds:correlation ${adv_opts.param_correlation}
    -algorithm:PeakPicker:thresholds:noise_level ${adv_opts.param_noise_level}
    -algorithm:PeakPicker:thresholds:search_radius ${adv_opts.param_search_radius}
    -algorithm:PeakPicker:wavelet_transform:spacing ${adv_opts.param_spacing}
    ${adv_opts.param_deconvolution}
    -algorithm:PeakPicker:deconvolution:asym_threshold ${adv_opts.param_asym_threshold}
    -algorithm:PeakPicker:deconvolution:left_width ${adv_opts.param_left_width}
    -algorithm:PeakPicker:deconvolution:right_width ${adv_opts.param_right_width}
    -algorithm:PeakPicker:deconvolution:scaling ${adv_opts.param_scaling}
    -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold}
    -algorithm:PeakPicker:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs}
    -algorithm:PeakPicker:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel}
    -algorithm:PeakPicker:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration}
    -algorithm:PeakPicker:deconvolution:fitting:penalties:position ${adv_opts.param_position}
    -algorithm:PeakPicker:deconvolution:fitting:penalties:height ${adv_opts.param_height}
    -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width}
    -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements}
    -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="input peak or raw data file " help="(-in)"/>
    <param name="param_ext_calibrants" type="data" format="mzML" optional="False" label="input file containing the external calibrant spectra (peak or raw data)#br#" help="(-ext_calibrants)"/>
    <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses)"/>
    <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants. These can be either two or three constants#br#per set, depending on the conversion type. Either one set for all calibrant spectra #br#(tab separated), or one for each spectrum.#br#For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)" help="(-tof_const)"/>
    <param name="param_peak_data" type="boolean" truevalue="-peak_data true" falsevalue="-peak_data false" checked="false" optional="True" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)." help="(-peak_data)"/>
    <param name="param_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked." help="(-signal_to_noise)"/>
    <param name="param_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks." help="(-peak_width)"/>
    <param name="param_estimate_peak_width" type="boolean" truevalue="-algorithm:PeakPicker:estimate_peak_width true" falsevalue="-algorithm:PeakPicker:estimate_peak_width false" checked="false" optional="True" label="Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored." help="(-estimate_peak_width)"/>
    <expand macro="advanced_options">
      <param name="param_centroid_percentage" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="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." help="(-centroid_percentage)"/>
      <param name="param_fwhm_lower_bound_factor" type="float" min="0.0" optional="True" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded." help="(-fwhm_lower_bound_factor)"/>
      <param name="param_fwhm_upper_bound_factor" type="float" min="0.0" optional="True" value="20.0" label="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." help="(-fwhm_upper_bound_factor)"/>
      <param name="param_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations)"/>
      <param name="param_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " help="(-position)"/>
      <param name="param_left_width" type="float" min="0.0" optional="True" value="1.0" label="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." help="(-left_width)"/>
      <param name="param_right_width" type="float" min="0.0" optional="True" value="1.0" label="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." help="(-right_width)"/>
      <param name="param_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized." help="(-height)"/>
      <param name="param_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz)"/>
      <param name="param_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluster" help="(-max_peak_distance)"/>
      <param name="param_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity." help="(-peak_bound)"/>
      <param name="param_peak_bound_ms2_level" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity for MS/MS peaks." help="(-peak_bound_ms2_level)"/>
      <param name="param_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." help="(-correlation)"/>
      <param name="param_noise_level" type="float" min="0.0" optional="True" value="0.1" label="noise level for the search of the peak endpoints." help="(-noise_level)"/>
      <param name="param_search_radius" type="integer" min="0" optional="True" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help="(-search_radius)"/>
      <param name="param_spacing" type="float" min="0.0" optional="True" value="0.001" label="spacing of the cwt." help="(-spacing)"/>
      <param name="param_deconvolution" type="boolean" truevalue="-algorithm:PeakPicker:deconvolution:deconvolution true" falsevalue="-algorithm:PeakPicker:deconvolution:deconvolution false" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help="(-deconvolution)"/>
      <param name="param_asym_threshold" type="float" min="0.0" optional="True" value="0.3" label="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." help="(-asym_threshold)"/>
      <param name="param_left_width" type="float" min="0.0" optional="True" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." help="(-left_width)"/>
      <param name="param_right_width" type="float" min="0.0" optional="True" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." help="(-right_width)"/>
      <param name="param_scaling" type="float" min="0.0" optional="True" value="0.12" label="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." help="(-scaling)"/>
      <param name="param_fwhm_threshold" type="float" min="0.0" optional="True" value="0.7" label="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." help="(-fwhm_threshold)"/>
      <param name="param_eps_abs" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the absolute error gets smaller than this value the fitting is stopped." help="(-eps_abs)"/>
      <param name="param_eps_rel" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the relative error gets smaller than this value the fitting is stopped." help="(-eps_rel)"/>
      <param name="param_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration)"/>
      <param name="param_position" type="float" min="0.0" optional="True" value="0.0" label="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." help="(-position)"/>
      <param name="param_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." help="(-height)"/>
      <param name="param_left_width" type="float" min="0.0" optional="True" value="0.0" label="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." help="(-left_width)"/>
      <param name="param_right_width" type="float" min="0.0" optional="True" value="0.0" label="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." help="(-right_width)"/>
      <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="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)." help="(-max_intensity)"/>
      <param name="param_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor)"/>
      <param name="param_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile)"/>
      <param name="param_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="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" help="(-auto_mode)"/>
      <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/>
      <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/>
      <param name="param_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp)"/>
      <param name="param_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements)"/>
      <param name="param_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="output file " format="mzML"/>
  </outputs>
  <help>**What it does**

Applies time of flight calibration.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html

@REFERENCES@
</help>
</tool>