Mercurial > repos > galaxyp > openms_internalcalibration

comparison InternalCalibration.xml @ 11:6c58aa0ed5c1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:00:38 +0000
parents cca2b6c3ae61
children f49a58e03ada
comparison
equal deleted inserted replaced
10:cca2b6c3ae61 11:6c58aa0ed5c1
148 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false"> 148 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
149 <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=""/> 149 <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=""/>
150 <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=""/> 150 <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=""/>
151 </section> 151 </section>
152 <expand macro="adv_opts_macro"> 152 <expand macro="adv_opts_macro">
153 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 153 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
154 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 154 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
155 <expand macro="list_string_san"/> 155 <expand macro="list_string_san"/>
156 </param> 156 </param>
157 </expand> 157 </expand>
158 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 158 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
159 <option value="lock_out_FLAG">lock_out (Plot image of pre- and post calibration errors)</option> 159 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
160 <option value="lock_fail_out_FLAG">lock_fail_out (Plot image of pre- and post calibration errors)</option> 160 <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>
161 <option value="models_FLAG">models (Plot image of pre- and post calibration errors)</option> 161 <option value="models_FLAG">models (Table of model parameters for each spectrum)</option>
162 <option value="models_plot_FLAG">models_plot (Plot image of pre- and post calibration errors)</option> 162 <option value="models_plot_FLAG">models_plot (Plot image of model parameters for each spectrum)</option>
163 <option value="residuals_FLAG">residuals (Plot image of pre- and post calibration errors)</option> 163 <option value="residuals_FLAG">residuals (Table of pre- and post calibration errors)</option>
164 <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option> 164 <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
165 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 165 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
166 </param> 166 </param>
167 </inputs> 167 </inputs>
168 <outputs> 168 <outputs>
194 <expand macro="manutest_InternalCalibration"/> 194 <expand macro="manutest_InternalCalibration"/>
195 </tests> 195 </tests>
196 <help><![CDATA[Applies an internal mass recalibration. 196 <help><![CDATA[Applies an internal mass recalibration.
197 197
198 198
199 For more information, visit http://www.openms.de/documentation/TOPP_InternalCalibration.html]]></help> 199 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_InternalCalibration.html]]></help>
200 <expand macro="references"/> 200 <expand macro="references"/>
201 </tool> 201 </tool>