Mercurial > repos > iuc > data_manager_hisat2_index_builder
comparison data_manager/hisat2_index_builder.py @ 1:56f435c0b83e draft
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 16:00:23 -0400 |
| parents | 8dbde949a86d |
| children | e8239a46a579 |
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| 0:8dbde949a86d | 1:56f435c0b83e |
|---|---|
| 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() ) |