Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
changeset 10:d878e492546c draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 07 Sep 2018 20:03:30 -0400 |
| parents | 7cfce83a7f62 |
| children | b1e8f8a613e6 |
| files | data_manager/fetch_refseq.py data_manager/fetch_refseq.xml |
| diffstat | 2 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/fetch_refseq.py Fri Sep 07 19:57:47 2018 -0400 +++ b/data_manager/fetch_refseq.py Fri Sep 07 20:03:30 2018 -0400 @@ -131,18 +131,21 @@ parser.add_argument('--mol_types', nargs='+', 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: dm_opts = json.loads(open(args.galaxy_datamanager_filename).read()) output_directory = dm_opts['output_data'][0]['extra_files_path'] # take the extra_files_path of the first output parameter data_manager_dict = {} else: output_directory = args.output_directory - for division_name in args.division_names: + for division_name in division_names: if args.pin_date is not None: today_str = args.pin_date else: today_str = date.today().strftime('%Y-%m-%d') # ISO 8601 date format - [release_num, fasta_files] = get_refseq_division(division_name, args.mol_types, output_directory, args.debug, args.compress) + [release_num, fasta_files] = get_refseq_division(division_name, mol_types, output_directory, args.debug, args.compress) if args.galaxy_datamanager_filename is not None: for i, mol_type in enumerate(args.mol_types): assert mol_type in fasta_files[i], "Filename does not contain expected mol_type ({}, {})".format(mol_type, fasta_files[i])
--- a/data_manager/fetch_refseq.xml Fri Sep 07 19:57:47 2018 -0400 +++ b/data_manager/fetch_refseq.xml Fri Sep 07 20:03:30 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.10" tool_type="manage_data"> +<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.11" tool_type="manage_data"> <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description> <requirements> <requirement type="package" version="3">python</requirement>