comparison PeakPickerHiRes.xml @ 0:2741adc39601 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

0:2741adc39601

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Signal processing and preprocessing]-->
<tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.1.0">
  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">PeakPickerHiRes</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PeakPickerHiRes

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_signal_to_noise:
  -algorithm:signal_to_noise $param_algorithm_signal_to_noise
#end if

#if $rep_param_algorithm_ms_levels:
-algorithm:ms_levels
  #for token in $rep_param_algorithm_ms_levels:
    #if " " in str(token):
      "$token.param_algorithm_ms_levels"
    #else
      $token.param_algorithm_ms_levels
    #end if
  #end for
#end if
#if $param_algorithm_report_FWHM:
  -algorithm:report_FWHM
#end if
#if $param_algorithm_report_FWHM_unit:
  -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
#end if
#if $param_algorithm_SignalToNoise_win_len:
  -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
#end if
#if $param_algorithm_SignalToNoise_bin_count:
  -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
#end if
#if $param_algorithm_SignalToNoise_min_required_elements:
  -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
#end if
#if $param_algorithm_SignalToNoise_write_log_messages:
  -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_processOption:
  -processOption $adv_opts.param_processOption
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_spacing_difference_gap:
  -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
#end if
    #if $adv_opts.param_algorithm_spacing_difference:
  -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
#end if
    #if $adv_opts.param_algorithm_missing:
  -algorithm:missing $adv_opts.param_algorithm_missing
#end if
    #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
  -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
#end if
    #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
  -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
#end if
    #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
  -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
#end if
    #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
  -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
#end if
    #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
  -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
    <param name="param_algorithm_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 (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
    <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
      <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1 2" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/>
    <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative(ppm)" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
      <option value="absolute">absolute</option>
      <option value="relative(ppm)" selected="true">relative(ppm)</option>
    </param>
    <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
    <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
    <param name="param_algorithm_SignalToNoise_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_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_processOption" display="radio" type="select" optional="False" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) ">
        <option value="inmemory" selected="true">inmemory</option>
        <option value="lowmemory">lowmemory</option>
      </param>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_algorithm_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/>
      <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/>
      <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/>
      <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) 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 be added to the LAST histogram bin. 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). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
      <param name="param_algorithm_SignalToNoise_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_algorithm_SignalToNoise_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_algorithm_SignalToNoise_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_algorithm_SignalToNoise_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" format="mzml"/>
  </outputs>
  <help>Finds mass spectrometric peaks in profile mass spectra.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help>
</tool>