Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
changeset 11:b1e8f8a613e6 draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 07 Sep 2018 20:07:55 -0400 |
| parents | d878e492546c |
| children | 45baee31ca39 |
| files | data_manager/fetch_refseq.py data_manager/fetch_refseq.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- 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:
--- 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 @@ -<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.11" tool_type="manage_data"> +<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.12" 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>