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comparison searchgui.xml @ 58:07ff622ec007 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
author galaxyp
date Sat, 10 Apr 2021 15:57:17 +0000
parents da885ca16cb2
children 943a34df6047
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57:da885ca16cb2 58:07ff622ec007
168 ]]> 168 ]]>
169 </command> 169 </command>
170 <inputs> 170 <inputs>
171 <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/> 171 <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>
172 172
173 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file"/> 173 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>
174 174
175 <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists" 175 <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
176 help="Select appropriate MGF/MZML dataset(s) from history" /> 176 help="Select appropriate MGF/MZML dataset(s) from history" />
177 177
178 <!-- Search Engine Selection --> 178 <!-- Search Engine Selection -->
324 324
325 Default: X! Tandem and MS-GF+ are executed. 325 Default: X! Tandem and MS-GF+ are executed.
326 326
327 Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed. 327 Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
328 328
329 **Input FASTA**
330
331 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)
332 and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format:
333
334 >generic[your tag]|[protein accession]|[protein description]
335
336 or
337
338 >generic[your tag]|[protein accession]
339
340 See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta.
341
342
343
329 </help> 344 </help>
330 <expand macro="citations" /> 345 <expand macro="citations" />
331 </tool> 346 </tool>