Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.py @ 1:6ba1ec5f86fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be
author iuc
date Sat, 03 Aug 2019 05:31:12 -0400
parents e4cdf82de430
children edacc4bcd3cb
comparison
equal deleted inserted replaced
0:e4cdf82de430 1:6ba1ec5f86fc
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,