Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_database.py @ 19:ffeb852407d6 draft default tip
"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 6f21145d4103d33c227f52dc55a7d3dcf52f4f5d-dirty"
| author | dfornika |
|---|---|
| date | Wed, 23 Oct 2019 14:21:07 -0400 |
| parents | f005b6efd096 |
| children |
comparison
equal
deleted
inserted
replaced
| 18:f005b6efd096 | 19:ffeb852407d6 |
|---|---|
| 81 '--db', database_path | 81 '--db', database_path |
| 82 ] | 82 ] |
| 83 | 83 |
| 84 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | 84 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) |
| 85 | 85 |
| 86 args = [ | 86 if kraken2_args["clean"]: |
| 87 '--threads', str(kraken2_args["threads"]), | 87 args = [ |
| 88 '--clean', | 88 '--threads', str(kraken2_args["threads"]), |
| 89 '--db', database_path | 89 '--clean', |
| 90 ] | 90 '--db', database_path |
| 91 | 91 ] |
| 92 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | 92 |
| 93 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | |
| 93 | 94 |
| 94 data_table_entry = { | 95 data_table_entry = { |
| 95 'data_tables': { | 96 'data_tables': { |
| 96 data_table_name: [ | 97 data_table_name: [ |
| 97 { | 98 { |
| 193 '--db', database_path | 194 '--db', database_path |
| 194 ] | 195 ] |
| 195 | 196 |
| 196 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | 197 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) |
| 197 | 198 |
| 198 args = [ | 199 if kraken2_args["clean"]: |
| 199 '--threads', str(kraken2_args["threads"]), | 200 args = [ |
| 200 '--clean', | 201 '--threads', str(kraken2_args["threads"]), |
| 201 '--db', database_path | 202 '--clean', |
| 202 ] | 203 '--db', database_path |
| 203 | 204 ] |
| 204 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | 205 |
| 206 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | |
| 205 | 207 |
| 206 data_table_entry = { | 208 data_table_entry = { |
| 207 'data_tables': { | 209 'data_tables': { |
| 208 data_table_name: [ | 210 data_table_name: [ |
| 209 { | 211 { |
| 248 '--db', custom_database_name | 250 '--db', custom_database_name |
| 249 ] | 251 ] |
| 250 | 252 |
| 251 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | 253 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) |
| 252 | 254 |
| 253 args = [ | 255 if kraken2_args["clean"]: |
| 254 '--threads', str(kraken2_args["threads"]), | 256 args = [ |
| 255 '--clean', | 257 '--threads', str(kraken2_args["threads"]), |
| 256 '--db', custom_database_name | 258 '--clean', |
| 257 ] | 259 '--db', custom_database_name |
| 258 | 260 ] |
| 259 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | 261 |
| 262 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) | |
| 260 | 263 |
| 261 data_table_entry = { | 264 data_table_entry = { |
| 262 'data_tables': { | 265 'data_tables': { |
| 263 data_table_name: [ | 266 data_table_name: [ |
| 264 { | 267 { |
| 284 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') | 287 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') |
| 285 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)') | 288 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)') |
| 286 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') | 289 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') |
| 287 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') | 290 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') |
| 288 parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='') | 291 parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='') |
| 292 parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files') | |
| 289 args = parser.parse_args() | 293 args = parser.parse_args() |
| 290 | 294 |
| 291 data_manager_input = json.loads(open(args.data_manager_json).read()) | 295 data_manager_input = json.loads(open(args.data_manager_json).read()) |
| 292 | 296 |
| 293 target_directory = data_manager_input['output_data'][0]['extra_files_path'] | 297 target_directory = data_manager_input['output_data'][0]['extra_files_path'] |
| 306 kraken2_args = { | 310 kraken2_args = { |
| 307 "kmer_len": args.kmer_len, | 311 "kmer_len": args.kmer_len, |
| 308 "minimizer_len": args.minimizer_len, | 312 "minimizer_len": args.minimizer_len, |
| 309 "minimizer_spaces": args.minimizer_spaces, | 313 "minimizer_spaces": args.minimizer_spaces, |
| 310 "threads": args.threads, | 314 "threads": args.threads, |
| 315 "clean": args.clean, | |
| 311 } | 316 } |
| 312 data_manager_output = kraken2_build_standard( | 317 data_manager_output = kraken2_build_standard( |
| 313 kraken2_args, | 318 kraken2_args, |
| 314 target_directory, | 319 target_directory, |
| 315 ) | 320 ) |
| 323 "special_database_type": str(args.special_database_type), | 328 "special_database_type": str(args.special_database_type), |
| 324 "kmer_len": args.kmer_len, | 329 "kmer_len": args.kmer_len, |
| 325 "minimizer_len": args.minimizer_len, | 330 "minimizer_len": args.minimizer_len, |
| 326 "minimizer_spaces": args.minimizer_spaces, | 331 "minimizer_spaces": args.minimizer_spaces, |
| 327 "threads": args.threads, | 332 "threads": args.threads, |
| 333 "clean": args.clean, | |
| 328 } | 334 } |
| 329 data_manager_output = kraken2_build_special( | 335 data_manager_output = kraken2_build_special( |
| 330 kraken2_args, | 336 kraken2_args, |
| 331 target_directory, | 337 target_directory, |
| 332 ) | 338 ) |
| 336 "skip_maps": args.skip_maps, | 342 "skip_maps": args.skip_maps, |
| 337 "kmer_len": args.kmer_len, | 343 "kmer_len": args.kmer_len, |
| 338 "minimizer_len": args.minimizer_len, | 344 "minimizer_len": args.minimizer_len, |
| 339 "minimizer_spaces": args.minimizer_spaces, | 345 "minimizer_spaces": args.minimizer_spaces, |
| 340 "threads": args.threads, | 346 "threads": args.threads, |
| 347 "clean": args.clean, | |
| 341 } | 348 } |
| 342 data_manager_output = kraken2_build_custom( | 349 data_manager_output = kraken2_build_custom( |
| 343 kraken2_args, | 350 kraken2_args, |
| 344 args.custom_database_name, | 351 args.custom_database_name, |
| 345 target_directory, | 352 target_directory, |