comparison InternalCalibration.xml @ 11:6c58aa0ed5c1 draft

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

10:cca2b6c3ae61

    <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
      <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
      <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <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="true">
      <option value="lock_out_FLAG">lock_out (Plot image of pre- and post calibration errors)</option>
      <option value="lock_fail_out_FLAG">lock_fail_out (Plot image of pre- and post calibration errors)</option>
      <option value="models_FLAG">models (Plot image of pre- and post calibration errors)</option>
      <option value="models_plot_FLAG">models_plot (Plot image of pre- and post calibration errors)</option>
      <option value="residuals_FLAG">residuals (Plot image of pre- and post calibration errors)</option>
      <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>

    <expand macro="manutest_InternalCalibration"/>
  </tests>
  <help><![CDATA[Applies an internal mass recalibration.


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

11:6c58aa0ed5c1

    <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
      <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
      <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <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="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
      <option value="lock_fail_out_FLAG">lock_fail_out (Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in')</option>
      <option value="models_FLAG">models (Table of model parameters for each spectrum)</option>
      <option value="models_plot_FLAG">models_plot (Plot image of model parameters for each spectrum)</option>
      <option value="residuals_FLAG">residuals (Table of pre- and post calibration errors)</option>
      <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>

    <expand macro="manutest_InternalCalibration"/>
  </tests>
  <help><![CDATA[Applies an internal mass recalibration.


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