Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
changeset 2:3d628f1e1bef draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 04825a097d217d30deb5fcb6906fe718023e25b6"
| author | iuc |
|---|---|
| date | Tue, 28 Apr 2020 07:57:37 +0000 |
| parents | 8dd4076813ef |
| children | f7b443a73374 |
| files | data_manager/data_manager.py data_manager/ncbi_taxonomy_fetcher.xml |
| diffstat | 2 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/data_manager.py Tue Apr 04 17:50:42 2017 -0400 +++ b/data_manager/data_manager.py Tue Apr 28 07:57:37 2020 +0000 @@ -56,7 +56,8 @@ output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy')) for filename in os.listdir(workdir): shutil.move(os.path.join(output_path, filename), target_directory) - file(args.output, 'w').write(json.dumps(data_manager_json)) + with open(args.output, 'w') as out: + out.write(json.dumps(data_manager_json, sort_keys=True)) if __name__ == '__main__':
--- a/data_manager/ncbi_taxonomy_fetcher.xml Tue Apr 04 17:50:42 2017 -0400 +++ b/data_manager/ncbi_taxonomy_fetcher.xml Tue Apr 28 07:57:37 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.0"> +<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.1"> <description>taxonomy downloader</description> <command detect_errors="exit_code"> <![CDATA[ @@ -14,7 +14,7 @@ </command> <inputs> <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" /> - <param name="taxonomy_url" type="text" label="Enter URL for taxonomy files" /> + <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" />