Mercurial > repos > devteam > data_manager_picard_index_builder
changeset 6:fa8c605bf385 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
| author | iuc |
|---|---|
| date | Sun, 16 Apr 2023 08:28:16 +0000 |
| parents | acaa6719a478 |
| children | |
| files | data_manager/picard_index_builder.py data_manager_conf.xml |
| diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager/picard_index_builder.py Mon Feb 03 22:27:13 2020 +0000 +++ b/data_manager/picard_index_builder.py Sun Apr 16 08:28:16 2023 +0000 @@ -2,11 +2,11 @@ # Dan Blankenberg from __future__ import print_function +import json import optparse import os import subprocess import sys -from json import dumps, loads DEFAULT_DATA_TABLE_NAME = "picard_indexes" @@ -58,7 +58,8 @@ filename = args[0] - params = loads(open(filename).read()) + with open(filename) as fh: + params = json.load(fh) target_directory = params['output_data'][0]['extra_files_path'] os.mkdir(target_directory) data_manager_dict = {} @@ -75,7 +76,8 @@ sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME) # save info to json file - open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True)) + with open(filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__":
--- a/data_manager_conf.xml Mon Feb 03 22:27:13 2020 +0000 +++ b/data_manager_conf.xml Sun Apr 16 08:28:16 2023 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/picard_index_builder.xml" id="picard_index_builder" version="0.0.1"> + <data_manager tool_file="data_manager/picard_index_builder.xml" id="picard_index_builder"> <data_table name="picard_indexes"> <output> <column name="value" />