Mercurial > repos > galaxyp > openms_nucleicacidsearchengine

comparison NucleicAcidSearchEngine.xml @ 2:00b91aaec050 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:49:38 +0000
parents fe6eddc2e756
children 92864c71ac6a
comparison
equal deleted inserted replaced
1:0b91652c7743 2:00b91aaec050
361 <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/> 361 <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/>
362 <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/> 362 <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/>
363 </section> 363 </section>
364 <expand macro="adv_opts_macro"> 364 <expand macro="adv_opts_macro">
365 <param name="decharge_ms2" argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/> 365 <param name="decharge_ms2" argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/>
366 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 366 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
367 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 367 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
368 <expand macro="list_string_san"/> 368 <expand macro="list_string_san"/>
369 </param> 369 </param>
370 </expand> 370 </expand>
371 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 371 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
372 <option value="id_out_FLAG">id_out (Do not score hits to decoy sequences and remove them when filtering)</option> 372 <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option>
373 <option value="lfq_out_FLAG">lfq_out (Do not score hits to decoy sequences and remove them when filtering)</option> 373 <option value="lfq_out_FLAG">lfq_out (Output file: Targets for label-free quantification using FeatureFinderMetaboIdent ('id' input))</option>
374 <option value="theo_ms2_out_FLAG">theo_ms2_out (Do not score hits to decoy sequences and remove them when filtering)</option> 374 <option value="theo_ms2_out_FLAG">theo_ms2_out (Output file: theoretical MS2 spectra for precursor mass matches)</option>
375 <option value="exp_ms2_out_FLAG">exp_ms2_out (Do not score hits to decoy sequences and remove them when filtering)</option> 375 <option value="exp_ms2_out_FLAG">exp_ms2_out (Output file: experimental MS2 spectra for precursor mass matches)</option>
376 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 376 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
377 </param> 377 </param>
378 </inputs> 378 </inputs>
379 <outputs> 379 <outputs>
380 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 380 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
399 <expand macro="manutest_NucleicAcidSearchEngine"/> 399 <expand macro="manutest_NucleicAcidSearchEngine"/>
400 </tests> 400 </tests>
401 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra. 401 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra.
402 402
403 403
404 For more information, visit http://www.openms.de/documentation/UTILS_NucleicAcidSearchEngine.html]]></help> 404 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_NucleicAcidSearchEngine.html]]></help>
405 <expand macro="references"/> 405 <expand macro="references"/>
406 </tool> 406 </tool>