Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
changeset 4:fca4564d83ae draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 68adfad76cdb5ff13ec9fb49895a3cde2c502514"
| author | iuc |
|---|---|
| date | Sat, 24 Apr 2021 20:55:33 +0000 |
| parents | ea8b97163133 |
| children | d8c2fea65c76 |
| files | data_manager/install_primer_scheme_bedfiles.py data_manager/install_primer_scheme_bedfiles.xml |
| diffstat | 2 files changed, 7 insertions(+), 9 deletions(-) [+] |
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--- a/data_manager/install_primer_scheme_bedfiles.py Mon Oct 12 13:46:40 2020 +0000 +++ b/data_manager/install_primer_scheme_bedfiles.py Sat Apr 24 20:55:33 2021 +0000 @@ -135,7 +135,8 @@ ) exit(1) - config = json.load(open(args.galaxy_datamanager_filename)) + with open(args.galaxy_datamanager_filename) as fh: + config = json.load(fh) output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) if output_directory is None: output_directory = args.output_directory @@ -144,10 +145,7 @@ os.makedirs(output_directory) data_manager_dict = {} - data_manager_dict["data_tables"] = json.load( - open(args.galaxy_datamanager_filename) - ).get("data_tables", {}) - data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {}) + data_manager_dict["data_tables"] = config.get("data_tables", {}) data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[ "data_tables" ].get(DATA_TABLE_NAME, []) @@ -163,5 +161,5 @@ ) data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) - print(data_manager_dict) - json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w")) + with open(args.galaxy_datamanager_filename, "w") as fh: + json.dump(data_manager_dict, fh, sort_keys=True)
--- a/data_manager/install_primer_scheme_bedfiles.xml Mon Oct 12 13:46:40 2020 +0000 +++ b/data_manager/install_primer_scheme_bedfiles.xml Sat Apr 24 20:55:33 2021 +0000 @@ -3,7 +3,7 @@ <requirement type="package" version="2.24.0">requests</requirement> </requirements> <!-- fetch all the primers in one go --> - <command detect_errors="exit_code"> + <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/install_primer_scheme_bedfiles.py' '${output_file}' #if $input.input_type == "ARTIC" @@ -13,7 +13,7 @@ --primer_name '${input.primer_name}' --primer_description '${input.primer_description}' #end if - </command> + ]]></command> <inputs> <conditional name="input"> <param name="input_type" label="Choose the source for primer schemes" type="select">