Mercurial > repos > iuc > data_manager_hisat2_index_builder

comparison data_manager/hisat2_index_builder.py @ 3:98a60a4cfb9a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 0efd33dc98b2632dfa5b5bcef71f463951c1e38e-dirty
author iuc
date Mon, 23 Nov 2015 09:41:52 -0500
parents b13b84cb11b5
children d210e1f185bd
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2:4014cb2c17db 3:98a60a4cfb9a
60 parser.add_argument( '--output', dest='output', action='store', type=str, default=None ) 60 parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
61 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None ) 61 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
62 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) 62 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
63 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) 63 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
64 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' ) 64 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' )
65 parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default=None ) 65 parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default='' )
66 options = parser.parse_args() 66 options = parser.parse_args()
67 67
68 filename = options.output 68 filename = options.output
69 69
70 params = loads( open( filename ).read() ) 70 params = loads( open( filename ).read() )