Mercurial > repos > diodupima > data_manager_coast_taxonomic_filters
changeset 15:3915837f12bb draft
"planemo upload commit 8f9b7580dc80c99bc735ea899819ff1d109de311-dirty"
| author | diodupima |
|---|---|
| date | Thu, 15 Jul 2021 13:15:00 +0000 |
| parents | b2fb92399590 |
| children | b9193300ac54 |
| files | ho2s.py txids_dm.xml |
| diffstat | 2 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/ho2s.py Thu Jul 15 12:11:19 2021 +0000 +++ b/ho2s.py Thu Jul 15 13:15:00 2021 +0000 @@ -4,6 +4,7 @@ from shutil import unpack_archive import datetime import subprocess +import json from galaxy.util.json import from_json_string, to_json_string @@ -17,7 +18,9 @@ type=str) args = parser.parse_args() - params = from_json_string(open(args.file).read()) + with open(args.file) as params_file: + params = json.load(params_file) + target_directory = params["output_data"][0]["extra_files_path"] os.mkdir(target_directory) @@ -48,7 +51,7 @@ "data_tables": {tool_data_table_name: [data_table_entry]} } output_json = open(args.file, "w") - output_json.write(to_json_string(data_manager_dict)) + output_json.write(json.dumps(data_manager_dict)) output_json.close()
--- a/txids_dm.xml Thu Jul 15 12:11:19 2021 +0000 +++ b/txids_dm.xml Thu Jul 15 13:15:00 2021 +0000 @@ -3,6 +3,7 @@ </description> <requirements> <requirement type="package" version="0.8">taxonkit</requirement> + <requirement type="package" version="3.7">python</requirement> </requirements> <command>python3 '$__tool_directory__/ho2s.py' --file "${out_file}" --tool_data_table_name "coast_taxonomic_filters"</command> <inputs>