Mercurial > repos > iuc > data_manager_hisat2_index_builder
changeset 6:f2ff73198a63 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author | iuc |
---|---|
date | Sun, 16 Apr 2023 08:27:15 +0000 |
parents | 721a2a97f31b |
children | |
files | data_manager/hisat2_index_builder.py data_manager_conf.xml |
diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager/hisat2_index_builder.py Mon Nov 18 22:22:10 2019 +0000 +++ b/data_manager/hisat2_index_builder.py Sun Apr 16 08:27:15 2023 +0000 @@ -3,11 +3,11 @@ from __future__ import print_function import argparse +import json import os import shlex import subprocess import sys -from json import dumps, loads DEFAULT_DATA_TABLE_NAME = "hisat2_indexes" @@ -66,7 +66,8 @@ filename = options.output - params = loads(open(filename).read()) + with open(filename) as fh: + params = json.load(fh) data_manager_dict = {} if options.fasta_dbkey in [None, '', '?']: @@ -78,7 +79,8 @@ build_hisat_index(data_manager_dict, options, params, sequence_id, sequence_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 Nov 18 22:22:10 2019 +0000 +++ b/data_manager_conf.xml Sun Apr 16 08:27:15 2023 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/hisat2_index_builder.xml" id="hisat2_index_builder" version="0.0.1"> + <data_manager tool_file="data_manager/hisat2_index_builder.xml" id="hisat2_index_builder"> <data_table name="hisat2_indexes"> <output> <column name="value" />