Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff 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 |
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--- a/data_manager/kraken2_build_database.py Fri May 24 13:39:08 2019 -0400 +++ b/data_manager/kraken2_build_database.py Wed Oct 23 14:21:07 2019 -0400 @@ -83,13 +83,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -195,13 +196,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_path + ] - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -250,13 +252,14 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', custom_database_name - ] + if kraken2_args["clean"]: + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', custom_database_name + ] - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { 'data_tables': { @@ -286,6 +289,7 @@ parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='') + parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files') args = parser.parse_args() data_manager_input = json.loads(open(args.data_manager_json).read()) @@ -308,6 +312,7 @@ "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, + "clean": args.clean, } data_manager_output = kraken2_build_standard( kraken2_args, @@ -325,6 +330,7 @@ "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, + "clean": args.clean, } data_manager_output = kraken2_build_special( kraken2_args, @@ -338,6 +344,7 @@ "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, + "clean": args.clean, } data_manager_output = kraken2_build_custom( kraken2_args,