comparison data_manager/kraken2_build_database.py @ 13:e9ee4d074d5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
author iuc
date Fri, 15 Nov 2024 22:31:29 +0000
parents 90b4d4f0a3a4
children 8c533e19b697
comparison
equal deleted inserted replaced
12:90b4d4f0a3a4 13:e9ee4d074d5d
26 26
27 class KrakenDatabaseTypes(Enum): 27 class KrakenDatabaseTypes(Enum):
28 standard_local_build = 'standard_local_build' 28 standard_local_build = 'standard_local_build'
29 standard_prebuilt = 'standard_prebuilt' 29 standard_prebuilt = 'standard_prebuilt'
30 minikraken = 'minikraken' 30 minikraken = 'minikraken'
31 special_prebuilt = 'special_prebuilt'
31 special = 'special' 32 special = 'special'
32 custom = 'custom' 33 custom = 'custom'
33 34
34 def __str__(self): 35 def __str__(self):
35 return self.value 36 return self.value
62 pluspf_08gb = "pluspf_08gb" 63 pluspf_08gb = "pluspf_08gb"
63 pluspf_16gb = "pluspf_16gb" 64 pluspf_16gb = "pluspf_16gb"
64 pluspfp = "pluspfp" 65 pluspfp = "pluspfp"
65 pluspfp_08gb = "pluspfp_08gb" 66 pluspfp_08gb = "pluspfp_08gb"
66 pluspfp_16gb = "pluspfp_16gb" 67 pluspfp_16gb = "pluspfp_16gb"
68 eupathdb48 = "eupathdb48"
67 69
68 def __str__(self): 70 def __str__(self):
69 return self.value 71 return self.value
70 72
71 73
142 'pluspf': "PlusPF (Standard plus protozoa and fungi)", 144 'pluspf': "PlusPF (Standard plus protozoa and fungi)",
143 'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)", 145 'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
144 'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)", 146 'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
145 'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)", 147 'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
146 'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)", 148 'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
147 'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)" 149 'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
150 'eupathdb48': "EuPathDB-46",
148 } 151 }
149 152
150 database_value = "_".join([ 153 database_value = "_".join([
151 now, 154 now,
152 "standard_prebuilt", 155 "standard_prebuilt",
406 parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces') 409 parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
407 parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor') 410 parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
408 parser.add_argument('--threads', dest='threads', default=1, help='threads') 411 parser.add_argument('--threads', dest='threads', default=1, help='threads')
409 parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build') 412 parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
410 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') 413 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
411 parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt.') 414 parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt or special_prebuilt.')
412 parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.') 415 parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
413 parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)') 416 parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
414 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') 417 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
415 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') 418 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
416 parser.add_argument('--custom-source-info', dest='custom_source_info', help='Description of how this build has been sourced (only applies to --database-type custom)') 419 parser.add_argument('--custom-source-info', dest='custom_source_info', help='Description of how this build has been sourced (only applies to --database-type custom)')
444 } 447 }
445 data_manager_output = kraken2_build_standard( 448 data_manager_output = kraken2_build_standard(
446 kraken2_args, 449 kraken2_args,
447 target_directory, 450 target_directory,
448 ) 451 )
449 elif str(args.database_type) == 'standard_prebuilt': 452 elif str(args.database_type) in ('standard_prebuilt', 'special_prebuilt'):
450 data_manager_output = kraken2_build_standard_prebuilt( 453 data_manager_output = kraken2_build_standard_prebuilt(
451 str(args.prebuilt_db), 454 str(args.prebuilt_db),
452 str(args.prebuilt_date), 455 str(args.prebuilt_date),
453 target_directory 456 target_directory
454 ) 457 )