diff options
| author | Pjotr Prins | 2021-01-04 10:25:36 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-04 10:25:36 +0000 |
| commit | f9f27a787fef0ad58c1ae465d8ba1ee4634083ae (patch) | |
| tree | 64bba4b6c496c9aa63aeb651bcc8252256a905bf /workflows/tools/normalize-yamlfa.py | |
| parent | bf8f13af6f083d382b4a3900566ef5e329084cbf (diff) | |
| download | bh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.tar.gz bh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.tar.lz bh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.zip | |
mapping: no longer requires specimen file for genbank output
Diffstat (limited to 'workflows/tools/normalize-yamlfa.py')
| -rwxr-xr-x | workflows/tools/normalize-yamlfa.py | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/workflows/tools/normalize-yamlfa.py b/workflows/tools/normalize-yamlfa.py index e3f92c0..20c2feb 100755 --- a/workflows/tools/normalize-yamlfa.py +++ b/workflows/tools/normalize-yamlfa.py @@ -3,7 +3,7 @@ # # Example: # -# python3 ./workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json MW241349 --species ./scripts/dict_ontology_standardization/ncbi_host_species.csv +# python3 ./workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json --species ncbi_host_species.csv --specimen specimen.csv --validate import argparse import json @@ -30,7 +30,7 @@ won't stop - it is used for (automated) uploads. parser.add_argument('-s','--state', type=str, help='State file (JSON) as produced by transform2yamlfa', required=True) parser.add_argument('--species', type=str, help='Species mapping file') -parser.add_argument('--specimen', type=str, help='Specimen mapping file') +parser.add_argument('--specimen', type=str, help='Optional specimen mapping file') parser.add_argument('--validate', action='store_true', help='Validation mode - stops on warning') parser.add_argument('--rewrite', action='store_true', help='Rewrite mode - updates files') parser.add_argument('--yaml', action='store_true', help='Input YAML instead of JSON') |