# HG changeset patch # User sanbi-uwc # Date 1536365275 14400 # Node ID b1e8f8a613e69f9981c022a4253efbacc8442ee3 # Parent d878e492546ce0955a9df95ce5203ae1ba8d5f33 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty diff -r d878e492546c -r b1e8f8a613e6 data_manager/fetch_refseq.py --- a/data_manager/fetch_refseq.py Fri Sep 07 20:03:30 2018 -0400 +++ b/data_manager/fetch_refseq.py Fri Sep 07 20:07:55 2018 -0400 @@ -127,11 +127,11 @@ parser.add_argument('--compress', default=False, action='store_true', help='Compress output files') parser.add_argument('--output_directory', default='tmp', help='Directory to write output to') parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs') - parser.add_argument('--division_names', nargs='+', help='RefSeq divisions to download') - parser.add_argument('--mol_types', nargs='+', help='Molecule types (genomic, rna, protein) to fetch') + parser.add_argument('--division_names', help='RefSeq divisions to download') + parser.add_argument('--mol_types', help='Molecule types (genomic, rna, protein) to fetch') parser.add_argument('--pin_date', help='Force download date to this version string') args = parser.parse_args() - + division_names = args.division_names.split(',') mol_types = args.mol_types.split(',') if args.galaxy_datamanager_filename is not None: diff -r d878e492546c -r b1e8f8a613e6 data_manager/fetch_refseq.xml --- a/data_manager/fetch_refseq.xml Fri Sep 07 20:03:30 2018 -0400 +++ b/data_manager/fetch_refseq.xml Fri Sep 07 20:07:55 2018 -0400 @@ -1,4 +1,4 @@ - + Fetch FASTA data from NCBI RefSeq and update all_fasta data table python