Mercurial > repos > iuc > data_manager_star_index_builder
comparison data_manager/rna_star_index_builder.py @ 6:64deddb6a8ec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author | iuc |
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date | Thu, 28 Nov 2019 15:48:56 -0500 |
parents | f5eb9afa8f8a |
children | d3879aceba04 |
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5:f5eb9afa8f8a | 6:64deddb6a8ec |
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4 import json | 4 import json |
5 | 5 |
6 | 6 |
7 def main(): | 7 def main(): |
8 parser = argparse.ArgumentParser() | 8 parser = argparse.ArgumentParser() |
9 parser.add_argument( '--config-file' ) | 9 parser.add_argument('--config-file') |
10 parser.add_argument( '--value' ) | 10 parser.add_argument('--value') |
11 parser.add_argument( '--dbkey' ) | 11 parser.add_argument('--dbkey') |
12 parser.add_argument( '--name' ) | 12 parser.add_argument('--name') |
13 parser.add_argument( '--subdir' ) | 13 parser.add_argument('--subdir') |
14 parser.add_argument( '--data-table' ) | 14 parser.add_argument('--data-table') |
15 parser.add_argument( '--with-gene-model', action='store_true' ) | 15 parser.add_argument('--with-gene-model', action='store_true') |
16 parser.add_argument( '--index-version' ) | 16 parser.add_argument('--index-version') |
17 | 17 |
18 args = parser.parse_args() | 18 args = parser.parse_args() |
19 | 19 |
20 if args.dbkey in [ None, '', '?' ]: | 20 if args.dbkey in [None, '', '?']: |
21 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( args.dbkey ) ) | 21 raise Exception( |
22 '"%s" is not a valid dbkey. You must specify a valid dbkey.' | |
23 % (args.dbkey) | |
24 ) | |
22 | 25 |
23 with_gene_model = "0" | 26 with_gene_model = "0" |
24 if args.with_gene_model: | 27 if args.with_gene_model: |
25 with_gene_model = "1" | 28 with_gene_model = "1" |
26 | 29 |
27 data_manager_dict = {'data_tables': {args.data_table: [dict({"value": args.value, "dbkey": args.dbkey, "name": args.name, "path": args.subdir, "with_gene_model": with_gene_model, "version": args.index_version} )]}} | 30 data_manager_dict = { |
28 open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) ) | 31 'data_tables': { |
32 args.data_table: [ | |
33 { | |
34 "value": args.value, | |
35 "dbkey": args.dbkey, | |
36 "name": args.name, | |
37 "path": args.subdir, | |
38 "with_gene_model": with_gene_model, | |
39 "version": args.index_version | |
40 } | |
41 ] | |
42 } | |
43 } | |
44 open(args.config_file, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) | |
29 | 45 |
30 | 46 |
31 if __name__ == "__main__": | 47 if __name__ == "__main__": |
32 main() | 48 main() |