Mercurial > repos > computational-metabolomics > mspurity_spectralmatching
comparison spectralMatching.xml @ 6:fecfe8c80e25 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author | computational-metabolomics |
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date | Thu, 04 Mar 2021 12:32:11 +0000 |
parents | aee10d29e82c |
children |
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5:829af6fecd96 | 6:fecfe8c80e25 |
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219 from_work_dir="xcms_matched_results.tsv" /> | 219 from_work_dir="xcms_matched_results.tsv" /> |
220 </outputs> | 220 </outputs> |
221 <tests> | 221 <tests> |
222 <test> | 222 <test> |
223 <param name="q_dbPth" value="createDatabase_output.sqlite" /> | 223 <param name="q_dbPth" value="createDatabase_output.sqlite" /> |
224 <param name="q_spectraTypes_bool" value="true" /> | |
225 <param name="q_spectraTypes" value="inter,av_all" /> | |
224 <param name="l_dbPth_select" value="userdb" /> | 226 <param name="l_dbPth_select" value="userdb" /> |
225 <param name="l_dbPth" value="PR100037.sqlite" /> | 227 <param name="l_dbPth" value="PR100037.sqlite" /> |
226 <param name="q_xcmsGroups_bool" value="true" /> | 228 <param name="q_xcmsGroups_bool" value="true" /> |
227 <param name="l_accessions_bool" value="true" /> | 229 <param name="l_accessions_bool" value="true" /> |
228 <param name="q_xcmsGroups" value="14" /> | 230 <param name="q_xcmsGroups" value="14" /> |
232 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/> | 234 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/> |
233 </test> | 235 </test> |
234 <test> | 236 <test> |
235 <param name="l_instrumentTypes_bool" value="true" /> | 237 <param name="l_instrumentTypes_bool" value="true" /> |
236 <param name="q_dbPth" value="createDatabase_output.sqlite" /> | 238 <param name="q_dbPth" value="createDatabase_output.sqlite" /> |
239 <param name="q_spectraTypes_bool" value="true" /> | |
240 <param name="q_spectraTypes" value="inter,av_all" /> | |
237 <param name="l_dbPth_select" value="userdb" /> | 241 <param name="l_dbPth_select" value="userdb" /> |
238 <param name="l_dbPth" value="PR100037.sqlite" /> | 242 <param name="l_dbPth" value="PR100037.sqlite" /> |
239 <param name="q_xcmsGroups_bool" value="true" /> | 243 <param name="q_xcmsGroups_bool" value="true" /> |
240 <param name="l_accessions_bool" value="true" /> | 244 <param name="l_accessions_bool" value="true" /> |
241 <param name="q_xcmsGroups" value="14" /> | 245 <param name="q_xcmsGroups" value="14" /> |
358 All matched results from the query spectra to the library spectra. Contains the same as above | 362 All matched results from the query spectra to the library spectra. Contains the same as above |
359 without the XCMS details. This table is useful to observe spectral matching results | 363 without the XCMS details. This table is useful to observe spectral matching results |
360 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features. | 364 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features. |
361 | 365 |
362 | 366 |
363 .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html | 367 .. _spectral_database_schema: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html |
364 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases | 368 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases |
365 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases | 369 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases |
366 .. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html | 370 .. _msPurity_spectral_matching_vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html |
367 | 371 |
368 ]]></help> | 372 ]]></help> |
369 | 373 |
370 <expand macro="citations"> </expand> | 374 <expand macro="citations"> </expand> |
371 </tool> | 375 </tool> |