Mercurial > repos > iuc > data_manager_dada2

comparison data_manager/data_manager.py @ 3:c29275496061 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 8533fe71d1d50f09348da2dc34941724407a1ffe"
author iuc
date Tue, 14 Jul 2020 07:37:09 -0400
parents a6a81f921701
children 38ccd4589990
comparison
equal deleted inserted replaced
2:a6a81f921701 3:c29275496061
103 with open(outjson) as jf: 103 with open(outjson) as jf:
104 params = json.loads(jf.read()) 104 params = json.loads(jf.read())
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
110 data_manager_json = {"data_tables": {}} 110 data_manager_json = {"data_tables": {}}
111 data_manager_entry = {} 111 data_manager_entry = {}
112 data_manager_entry['value'] = dataset 112 data_manager_entry['value'] = dataset
113 data_manager_entry['name'] = FILE2NAME[dataset] 113 data_manager_entry['name'] = FILE2NAME[dataset]
114 data_manager_entry['path'] = dataset + ".taxonomy" 114 data_manager_entry['path'] = dataset + ".taxonomy"
115 data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS) 115 data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
116 data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry 116 data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
117 117
118 if FILE2SPECIESURL.get(dataset, False ): 118 if FILE2SPECIESURL.get(dataset, False):
119 url_download( FILE2SPECIESURL[dataset], dataset + ".species", workdir) 119 url_download(FILE2SPECIESURL[dataset], dataset + ".species", workdir)
120 data_manager_entry = {} 120 data_manager_entry = {}
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