Mercurial > repos > iuc > data_manager_selection_background
changeset 3:10ac95ec81d9 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit bbba39ae993250a1e7301965b03c12621513775e"
| author | iuc |
|---|---|
| date | Wed, 25 Aug 2021 21:07:59 +0000 |
| parents | e4f07770b340 |
| children | |
| files | data_manager/data_manager_selection_background.py data_manager/data_manager_selection_background.xml tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 14 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager/data_manager_selection_background.py Tue Aug 24 17:58:31 2021 +0000 +++ b/data_manager/data_manager_selection_background.py Wed Aug 25 21:07:59 2021 +0000 @@ -111,21 +111,24 @@ parser.add_argument('--dataset', dest='dataset', action='store', help='Path for the sequences') args = parser.parse_args() - - work_dir = os.getcwd() + dbkey = str(args.dbkey) if args.uri is not None: background_fasta = url_download(args.uri) else: background_fasta = args.dataset - table_entry = '%s.fa' % args.dbkey - shutil.copy(background_fasta, os.path.join(work_dir, table_entry)) + with open(args.output) as fh: + params = json.load(fh) + target_directory = params['output_data'][0]['extra_files_path'] + os.makedirs(target_directory, exist_ok=True) + table_entry = '%s.fa' % dbkey + shutil.copy(background_fasta, os.path.join(target_directory, table_entry)) # Update Data Manager JSON and write to file data_manager_entry = { 'data_tables': { - 'selection_background': {'value': args.dbkey, 'label': args.label, 'path': table_entry} + 'selection_background': {'value': dbkey, 'label': args.label, 'path': table_entry} } }
--- a/data_manager/data_manager_selection_background.xml Tue Aug 24 17:58:31 2021 +0000 +++ b/data_manager/data_manager_selection_background.xml Wed Aug 25 21:07:59 2021 +0000 @@ -1,10 +1,12 @@ <?xml version="1.0"?> -<tool id="data_manager_selection_background" name="Add background sequences" tool_type="manage_data" version="1.0.2"> +<tool id="data_manager_selection_background" name="Add background sequences" tool_type="manage_data" version="1.0.3"> <description>for selection analysis</description> <command detect_errors="exit_code"> <![CDATA[ - python '$__tool_directory__/data_manager_selection_background.py' --out '$selection_background_json' - --dbkey '${dbkey}' + python '$__tool_directory__/data_manager_selection_background.py' --output '$selection_background_json' + #if $dbkey: + --dbkey '${dbkey}' + #end if --label '${label}' #if $data_source.source_selector == 'history': --dataset '$data_source.dataset'
--- a/tool_data_table_conf.xml.sample Tue Aug 24 17:58:31 2021 +0000 +++ b/tool_data_table_conf.xml.sample Wed Aug 25 21:07:59 2021 +0000 @@ -1,6 +1,6 @@ <tables> <!-- Locations of background sequences for clade analysis --> - <table name="selection_background" comment_char="#"> + <table allow_duplicate_entries="False" name="selection_background" comment_char="#"> <columns>value, label, path</columns> <file path="tool-data/selection_background.loc" /> </table>