Mercurial > repos > iuc > data_manager_hisat2_index_builder

comparison data_manager/hisat2_index_builder.py @ 1:b13b84cb11b5 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 feb20045fb10de6cce2517784f52672322d4d9f8-dirty
author iuc
date Sat, 10 Oct 2015 16:01:18 -0400
parents d3eb4d51b285
children 98a60a4cfb9a
comparison
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0:d3eb4d51b285 1:b13b84cb11b5
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, required=True, default=None ) 65 parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default=None )
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() )