comparison IDMassAccuracy.xml @ 13:31bc4129f589 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

12:f918cb7aefd5

    <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
    <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
    <expand macro="adv_opts_macro">
      <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
      <option value="out_precursor_FLAG">out_precursor (Enables the test mode (needed for internal use only))</option>
      <option value="out_fragment_FLAG">out_fragment (Enables the test mode (needed for internal use only))</option>
      <option value="out_precursor_fit_FLAG">out_precursor_fit (Enables the test mode (needed for internal use only))</option>
      <option value="out_fragment_fit_FLAG">out_fragment_fit (Enables the test mode (needed for internal use only))</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">

    <expand macro="manutest_IDMassAccuracy"/>
  </tests>
  <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.


For more information, visit http://www.openms.de/documentation/UTILS_IDMassAccuracy.html]]></help>
  <expand macro="references"/>
</tool>

13:31bc4129f589

    <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
    <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
    <expand macro="adv_opts_macro">
      <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="out_precursor_FLAG">out_precursor (Output file which contains the deviations from the precursors)</option>
      <option value="out_fragment_FLAG">out_fragment (Output file which contains the fragment ion m/z deviations)</option>
      <option value="out_precursor_fit_FLAG">out_precursor_fit (Gaussian fit to the histogram of mass deviations from the precursors)</option>
      <option value="out_fragment_fit_FLAG">out_fragment_fit (Gaussian fit to the histogram of mass deviations from the fragments)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">

    <expand macro="manutest_IDMassAccuracy"/>
  </tests>
  <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDMassAccuracy.html]]></help>
  <expand macro="references"/>
</tool>