Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 60:a6ff76e057fd 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/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003"
author galaxyp
date Tue, 20 Jul 2021 08:55:11 +0000
parents 943a34df6047
children 3ec27b4cee7c
comparison
equal deleted inserted replaced
59:943a34df6047 60:a6ff76e057fd
178 Remember to choose only .mzML files when using MetaMorpheus." /> 178 Remember to choose only .mzML files when using MetaMorpheus." />
179 179
180 <!-- Search Engine Selection --> 180 <!-- Search Engine Selection -->
181 <section name="search_engines_options" expanded="true" title="Search Engine Options"> 181 <section name="search_engines_options" expanded="true" title="Search Engine Options">
182 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> 182 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
183 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers. 183 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X.
184 MetaMorpheus only produce results when using mzML format.</help> 184 MetaMorpheus only produce results when using mzML format.</help>
185 <option value="X!Tandem" selected="True">X!Tandem</option> 185 <option value="X!Tandem" selected="True">X!Tandem</option>
186 <option value="MSGF" selected="True">MS-GF+</option> 186 <option value="MSGF" selected="True">MS-GF+</option>
187 <option value="OMSSA">OMSSA</option> 187 <option value="OMSSA">OMSSA</option>
188 <option value="Comet">Comet</option> 188 <option value="Comet">Comet</option>
239 <param name="input_parameters_file" value="Identification_Parameters_default.par"/> 239 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
240 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" /> 240 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
241 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/> 241 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
242 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 242 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
243 </test> 243 </test>
244 244
245 245
246 <!-- Test that search works with MetaMorpheus with default parameters works--> 246 <!-- Test that search works with MetaMorpheus with default parameters works-->
247 <!-- Test data has been taken from metamorpheus galaxy tool --> 247 <!-- Test data has been taken from metamorpheus galaxy tool -->
248 <test> 248 <test>
249 <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/> 249 <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/>
250 <param name="input_parameters_file" value="Identification_Parameters_default.par"/> 250 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
348 In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences) 348 In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences)
349 and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format: 349 and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format:
350 350
351 >generic[your tag]|[protein accession]|[protein description] 351 >generic[your tag]|[protein accession]|[protein description]
352 352
353 or 353 or
354 354
355 >generic[your tag]|[protein accession] 355 >generic[your tag]|[protein accession]
356 356
357 See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta. 357 See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta.
358 358