comparison PeakPickerHiRes.xml @ 1:94b97d2d98a4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

0:5ae104d0da6e

<?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>

#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:

#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:

#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) ">

1:94b97d2d98a4

<?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="2.2.0">
  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">PeakPickerHiRes</token>
    <import>macros.xml</import>
  </macros>

#end if
#if $param_algorithm_report_FWHM:
  -algorithm:report_FWHM
#end if
#if $param_algorithm_report_FWHM_unit:
  -algorithm:report_FWHM_unit
  #if " " in str($param_algorithm_report_FWHM_unit):
    "$param_algorithm_report_FWHM_unit"
  #else
    $param_algorithm_report_FWHM_unit
  #end if
#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:

#end if
#if $param_algorithm_SignalToNoise_min_required_elements:
  -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
#end if
#if $param_algorithm_SignalToNoise_write_log_messages:
  -algorithm:SignalToNoise:write_log_messages
  #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
    "$param_algorithm_SignalToNoise_write_log_messages"
  #else
    $param_algorithm_SignalToNoise_write_log_messages
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_processOption:
  -processOption
  #if " " in str($adv_opts.param_processOption):
    "$adv_opts.param_processOption"
  #else
    $adv_opts.param_processOption
  #end if
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_spacing_difference_gap:

#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="0.0" 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" 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" 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="relative" selected="true">relative</option>
      <option value="absolute">absolute</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) ">