Mercurial > repos > iuc > data_manager_metaphlan2_database_downloader
comparison data_manager/data_manager_metaphlan2_download.py @ 1:83f07f40b200 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan2_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author | iuc |
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date | Sun, 22 Nov 2020 12:51:11 +0000 |
parents | 9c4ad82be5bd |
children |
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0:9c4ad82be5bd | 1:83f07f40b200 |
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22 NB the directory pointed to by 'extra_files_path' | 22 NB the directory pointed to by 'extra_files_path' |
23 doesn't exist initially, it is the job of the script | 23 doesn't exist initially, it is the job of the script |
24 to create it if necessary. | 24 to create it if necessary. |
25 | 25 |
26 """ | 26 """ |
27 params = json.loads(open(jsonfile).read()) | 27 with open(jsonfile) as fh: |
28 params = json.load(fh) | |
28 return (params['param_dict'], | 29 return (params['param_dict'], |
29 params['output_data'][0]['extra_files_path']) | 30 params['output_data'][0]['extra_files_path']) |
30 | 31 |
31 | 32 |
32 # Utility functions for creating data table dictionaries | 33 # Utility functions for creating data table dictionaries |
34 # Example usage: | 35 # Example usage: |
35 # >>> d = create_data_tables_dict() | 36 # >>> d = create_data_tables_dict() |
36 # >>> add_data_table(d,'my_data') | 37 # >>> add_data_table(d,'my_data') |
37 # >>> add_data_table_entry(dict(dbkey='hg19',value='human')) | 38 # >>> add_data_table_entry(dict(dbkey='hg19',value='human')) |
38 # >>> add_data_table_entry(dict(dbkey='mm9',value='mouse')) | 39 # >>> add_data_table_entry(dict(dbkey='mm9',value='mouse')) |
39 # >>> print str(json.dumps(d)) | 40 # >>> print(json.dumps(d)) |
40 def create_data_tables_dict(): | 41 def create_data_tables_dict(): |
41 """Return a dictionary for storing data table information | 42 """Return a dictionary for storing data table information |
42 | 43 |
43 Returns a dictionary that can be used with 'add_data_table' | 44 Returns a dictionary that can be used with 'add_data_table' |
44 and 'add_data_table_entry' to store information about a | 45 and 'add_data_table_entry' to store information about a |
142 "metaphlan2_database", | 143 "metaphlan2_database", |
143 target_dir) | 144 target_dir) |
144 | 145 |
145 # Write output JSON | 146 # Write output JSON |
146 print("Outputting JSON") | 147 print("Outputting JSON") |
147 print(str(json.dumps(data_tables))) | 148 with open(jsonfile, 'w') as fh: |
148 with open(jsonfile, 'wb') as out: | 149 json.dump(data_tables, fh, sort_keys=True) |
149 out.write(json.dumps(data_tables)) | |
150 print("Done.") | 150 print("Done.") |