Mercurial > repos > sanbi-uwc > data_manager_fetch_artic_primers
changeset 1:59b3556d9ec8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
| author | sanbi-uwc |
|---|---|
| date | Thu, 16 Apr 2020 20:45:35 +0000 |
| parents | c401f63b3d12 |
| children | 119f459fc35f |
| files | data_manager/fetch_artic_primers.py data_manager/fetch_artic_primers.xml data_manager_conf.xml |
| diffstat | 3 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/fetch_artic_primers.py Thu Apr 16 14:06:59 2020 +0000 +++ b/data_manager/fetch_artic_primers.py Thu Apr 16 20:45:35 2020 +0000 @@ -19,13 +19,16 @@ } if not os.path.isdir(output_directory): - os.makedirs(output_directory) - data_manager_dict = json.load(open(output_filename)) + os.makedirs(output_directory) + data_manager_dict = {} + data_manager_dict['data_tables'] = json.load(open(output_filename)).get('data_tables', {}) data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) data_manager_dict['data_tables'][DATA_TABLE_NAME] = data_manager_dict['data_tables'].get(DATA_TABLE_NAME, []) data = [] for name, url in primer_sets.items(): + if name not in primers: + continue response = requests.get(url) if response.status_code != 200: print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)
--- a/data_manager/fetch_artic_primers.xml Thu Apr 16 14:06:59 2020 +0000 +++ b/data_manager/fetch_artic_primers.xml Thu Apr 16 20:45:35 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.1" tool_type="manage_data" profile="19.05"> +<tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.2" tool_type="manage_data" profile="19.05"> <requirements> <requirement type="package">python</requirement> <requirement type="package" version="2.22.0">requests</requirement> @@ -7,6 +7,7 @@ <command detect_errors="exit_code"> python '$__tool_directory__/fetch_artic_primers.py' --galaxy_datamanager_filename '${output_file}' + --primers '${primers}' </command> <inputs> <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch">
--- a/data_manager_conf.xml Thu Apr 16 14:06:59 2020 +0000 +++ b/data_manager_conf.xml Thu Apr 16 20:45:35 2020 +0000 @@ -8,9 +8,9 @@ <column name="path" output_ref="output_file" > <move type="file"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">artic_primers/#echo str($name).bed#</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">artic_primers/#echo str($value).bed#</target> </move> - <value_translation>artic_primers/#echo str($name).bed#</value_translation> + <value_translation>artic_primers/#echo str($value).bed#</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>