Mercurial > repos > dfornika > data_manager_mash_sketch_builder
annotate data_manager/mash_sketch_builder.py @ 0:647eedfd1556 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
author | dfornika |
---|---|
date | Sat, 22 Feb 2020 00:30:35 +0000 |
parents | |
children | af86557c1b87 |
rev | line source |
---|---|
0
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
1 #!/usr/bin/env python |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
2 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
3 import argparse |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
4 import errno |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
5 import json |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
6 import os |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
7 import subprocess |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
8 import sys |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
9 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
10 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
11 DATA_TABLE_NAME = "mash_sketches" |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
12 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
13 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
14 def mash_sketch(mash_sketch_args, sketch_name, target_directory, data_table_name=DATA_TABLE_NAME): |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
15 UUID = str(uuid.uuid4()) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
16 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
17 os.mkdir(os.path.join(target_directory, UUID)) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
18 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
19 sketch_path = os.path.join(UUID, "sketch"), |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
20 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
21 args = [ |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
22 '--threads', str(kraken2_args["threads"]), |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
23 '-k', str(mash_sketch_args["kmer_size"]), |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
24 '-s', str(mash_sketch_args["sketch_size"]), |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
25 '-o', sketch_path |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
26 ] |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
27 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
28 subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
29 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
30 if kraken2_args["clean"]: |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
31 args = [ |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
32 '--threads', str(kraken2_args["threads"]), |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
33 '--clean', |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
34 '--db', database_path |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
35 ] |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
36 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
37 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
38 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
39 data_table_entry = { |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
40 'data_tables': { |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
41 data_table_name: [ |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
42 { |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
43 "value": UUID, |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
44 "name": sketch_name, |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
45 "path": sketch_path, |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
46 } |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
47 ] |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
48 } |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
49 } |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
50 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
51 return data_table_entry |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
52 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
53 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
54 def main(): |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
55 parser = argparse.ArgumentParser() |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
56 parser.add_argument('data_manager_json') |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
57 parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length') |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
58 parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length') |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
59 parser.add_argument('--threads', dest='threads', default=1, help='threads') |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
60 parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch') |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
61 args = parser.parse_args() |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
62 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
63 data_manager_input = json.loads(open(args.data_manager_json).read()) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
64 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
65 target_directory = data_manager_input['output_data'][0]['extra_files_path'] |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
66 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
67 try: |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
68 os.mkdir( target_directory ) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
69 except OSError as exc: |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
70 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
71 pass |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
72 else: |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
73 raise |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
74 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
75 data_manager_output = {} |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
76 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
77 mash_sketch_args = { |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
78 "kmer_size": args.kmer_len, |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
79 "sketch_size": args.minimizer_len, |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
80 "threads": args.threads, |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
81 } |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
82 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
83 open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True)) |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
84 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
85 |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
86 if __name__ == "__main__": |
647eedfd1556
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 20558d9de7b6dd375a8835698f231cbc0c83446d-dirty"
dfornika
parents:
diff
changeset
|
87 main() |