Mercurial > repos > galaxyp > openms_openswathanalyzer

comparison OpenSwathAnalyzer.xml @ 11:7ca917175b23 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 19:43:44 +0000
parents bc57c90ba60f
children 08488066d588
comparison
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10:4da16805dea6 11:7ca917175b23
96 <option value="default" selected="true">default</option> 96 <option value="default" selected="true">default</option>
97 <option value="single_transition">single_transition</option> 97 <option value="single_transition">single_transition</option>
98 <expand macro="list_string_san"/> 98 <expand macro="list_string_san"/>
99 </param> 99 </param>
100 <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/> 100 <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
101 <param name="strict" argument="-algorithm:strict" type="text" optional="true" value="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help="">
102 <expand macro="list_string_san"/>
103 </param>
101 <section name="TransitionGroupPicker" title="" help="" expanded="false"> 104 <section name="TransitionGroupPicker" title="" help="" expanded="false">
102 <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> 105 <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
103 <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/> 106 <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
104 <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/> 107 <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
105 <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help=""> 108 <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
205 <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/> 208 <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/>
206 <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/> 209 <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
207 </section> 210 </section>
208 </section> 211 </section>
209 <expand macro="adv_opts_macro"> 212 <expand macro="adv_opts_macro">
210 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 213 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
211 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 214 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
212 <expand macro="list_string_san"/> 215 <expand macro="list_string_san"/>
213 </param> 216 </param>
214 </expand> 217 </expand>
215 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 218 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
216 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 219 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
217 </param> 220 </param>
218 </inputs> 221 </inputs>
219 <outputs> 222 <outputs>
220 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 223 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
227 <expand macro="manutest_OpenSwathAnalyzer"/> 230 <expand macro="manutest_OpenSwathAnalyzer"/>
228 </tests> 231 </tests>
229 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment. 232 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
230 233
231 234
232 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathAnalyzer.html]]></help> 235 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
233 <expand macro="references"/> 236 <expand macro="references"/>
234 </tool> 237 </tool>