# HG changeset patch # User dfornika # Date 1582578668 0 # Node ID 9e119de8edf45c34e3b62148c907eb1aab1ccd39 # Parent c842c12e81d99c133f92564a14a9fffebd18d9ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 3a2663e8a2d8b056e041c3c9e550d8e522f44583-dirty" diff -r c842c12e81d9 -r 9e119de8edf4 data_manager/mash_sketch_builder.py --- a/data_manager/mash_sketch_builder.py Mon Feb 24 19:17:36 2020 +0000 +++ b/data_manager/mash_sketch_builder.py Mon Feb 24 21:11:08 2020 +0000 @@ -27,6 +27,9 @@ '-p', str(mash_sketch_args["threads"]), str(mash_sketch_args["fasta"]), ] + + if mash_sketch_args["individual_sequences"]: + args = args + ["-i"] subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory) @@ -50,6 +53,7 @@ parser.add_argument('data_manager_json') parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length') parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length') + parser.add_argument('--individual-sequences', dest='individual_sequences', type=boolean, action='store_true' help='Sketch individual sequences (for multi-fasta files)') parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch') parser.add_argument('--threads', dest='threads', default=1, help='threads') parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch') @@ -59,8 +63,6 @@ target_directory = data_manager_input['output_data'][0]['extra_files_path'] - pprint("***" + target_directory + "***" ) - try: os.mkdir( target_directory ) except OSError as exc: @@ -75,6 +77,7 @@ "kmer_size": args.kmer_size, "sketch_size": args.sketch_size, "fasta": args.fasta, + "individual_sequences": args.individual_sequences, "threads": args.threads, } diff -r c842c12e81d9 -r 9e119de8edf4 data_manager/mash_sketch_builder.xml --- a/data_manager/mash_sketch_builder.xml Mon Feb 24 19:17:36 2020 +0000 +++ b/data_manager/mash_sketch_builder.xml Mon Feb 24 21:11:08 2020 +0000 @@ -18,6 +18,7 @@ --sketch-name '${sketch_name}' --sketch-size '${sketch_size}' --kmer-size '${kmer_size}' + ${individual_sequences} ]]> @@ -40,6 +41,7 @@ + @@ -51,8 +53,15 @@ - - + 10.1186/s13059-016-0997-x