Mercurial > repos > iuc > data_manager_dada2
comparison data_manager/data_manager.py @ 4:38ccd4589990 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author | iuc |
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date | Sun, 22 Nov 2020 12:47:30 +0000 |
parents | c29275496061 |
children |
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3:c29275496061 | 4:38ccd4589990 |
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98 shutil.copyfileobj(f_in, f_out) | 98 shutil.copyfileobj(f_in, f_out) |
99 | 99 |
100 | 100 |
101 def remote_dataset(dataset, outjson): | 101 def remote_dataset(dataset, outjson): |
102 | 102 |
103 with open(outjson) as jf: | 103 with open(outjson) as fh: |
104 params = json.loads(jf.read()) | 104 params = json.load(fh) |
105 | 105 |
106 workdir = params['output_data'][0]['extra_files_path'] | 106 workdir = params['output_data'][0]['extra_files_path'] |
107 os.mkdir(workdir) | 107 os.mkdir(workdir) |
108 url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) | 108 url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) |
109 | 109 |
121 data_manager_entry['value'] = dataset | 121 data_manager_entry['value'] = dataset |
122 data_manager_entry['name'] = FILE2NAME[dataset] | 122 data_manager_entry['name'] = FILE2NAME[dataset] |
123 data_manager_entry['path'] = dataset + ".species" | 123 data_manager_entry['path'] = dataset + ".species" |
124 data_manager_json["data_tables"]["dada2_species"] = data_manager_entry | 124 data_manager_json["data_tables"]["dada2_species"] = data_manager_entry |
125 | 125 |
126 with open(outjson, 'w') as jf: | 126 with open(outjson, 'w') as fh: |
127 jf.write(json.dumps(data_manager_json, sort_keys=True)) | 127 json.dump(data_manager_json, fh, sort_keys=True) |
128 | 128 |
129 | 129 |
130 if __name__ == '__main__': | 130 if __name__ == '__main__': |
131 parser = argparse.ArgumentParser(description='Create data manager json.') | 131 parser = argparse.ArgumentParser(description='Create data manager json.') |
132 parser.add_argument('--out', action='store', help='JSON filename') | 132 parser.add_argument('--out', action='store', help='JSON filename') |