Mercurial > repos > wolma > rnastar_index_builder

comparison data_manager/rna_star_index_builder.py @ 4:039890bdcb62 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 93138516106c74b1ccc70d2d946e6eaa29c7c1a3-dirty
author wolma
date Wed, 16 Oct 2019 03:33:53 -0400
parents 6127cd38980b
children bb74adafc98f
comparison
equal deleted inserted replaced
3:80bbca356b76 4:039890bdcb62
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 = {
31 'data_tables': {
32 args.data_table: [
33 {
34 "value": args.value,
35 "dbkey": args.dbkey,
36 "name": args.name,
37 "subdir": args.subdir,
38 "with_gene_model": with_gene_model,
39 "version": args.index_version
40 }
41 ]
42 }
43 }
28 open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) ) 44 open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) )
29 45
30 46
31 if __name__ == "__main__": 47 if __name__ == "__main__":
32 main() 48 main()