# HG changeset patch # User greg # Date 1583775739 14400 # Node ID 3fbd172e4055bc98da444680198f08b20e25bd5f Uploaded diff -r 000000000000 -r 3fbd172e4055 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Mon Mar 09 13:42:19 2020 -0400 @@ -0,0 +1,10 @@ +name: data_manager_vsnp_excel_filter +owner: greg +description: Data manager to download vSNP analysis Excel filter file +homepage_url: https://github.com/USDA-VS/vSNP +long_description: | + vSNP generates annotated SNP tables, this data manager installs the vSNP Excel filter file. +remote_repository_url: "https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/data_managers/vsnp_excel_filter" +type: unrestricted +categories: +- Data Managers diff -r 000000000000 -r 3fbd172e4055 data_manager/vsnp_excel_filter_fetcher.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/vsnp_excel_filter_fetcher.py Mon Mar 09 13:42:19 2020 -0400 @@ -0,0 +1,66 @@ +import argparse +import json +import os +import sys +try: + # For Python 3.0 and later + from urllib.request import Request, urlopen +except ImportError: + # Fall back to Python 2 imports + from urllib2 import Request, urlopen + + +def url_download(url, workdir): + file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url))) + src = None + dst = None + try: + req = Request(url) + src = urlopen(req) + with open(file_path, 'wb') as dst: + while True: + chunk = src.read(2**10) + if chunk: + dst.write(chunk) + else: + break + except Exception as e: + sys.exit(str(e)) + finally: + if src: + src.close() + return file_path + + +def download(dbkey, name, url, out_file): + + with open(out_file) as fh: + params = json.loads(fh.read()) + + workdir = params['output_data'][0]['extra_files_path'] + os.makedirs(workdir) + file_path = url_download(url, workdir) + entry_name = os.path.basename(file_path) + + data_manager_json = {"data_tables": {}} + data_manager_entry = {} + data_manager_entry['value'] = dbkey + data_manager_entry['name'] = entry_name + data_manager_entry['path'] = file_path + data_manager_entry['description'] = "Excel Filter file for %s" % name + data_manager_json["data_tables"]["vsnp_excel_filter"] = data_manager_entry + + with open(out_file, 'w') as fh: + fh.write(json.dumps(data_manager_json, sort_keys=True)) + + +parser = argparse.ArgumentParser() + +parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey') +parser.add_argument('--name', dest='name', help='Reference display name') +parser.add_argument('--url', dest='url', help='URL to download Excel file') +parser.add_argument('--out_file', dest='out_file', help='JSON output file') + +args = parser.parse_args() + +download(args.dbkey, args.name, args.url, args.out_file) diff -r 000000000000 -r 3fbd172e4055 data_manager/vsnp_excel_filter_fetcher.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/vsnp_excel_filter_fetcher.xml Mon Mar 09 13:42:19 2020 -0400 @@ -0,0 +1,101 @@ + + + Download vSNP Excel files + + python + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 3fbd172e4055 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Mar 09 13:42:19 2020 -0400 @@ -0,0 +1,21 @@ + + + + + + + + + + ${path} + vsnp/${value}/excel_filter/${name} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/vsnp/${value}/excel_filter/${name} + abspath + + + + + + + diff -r 000000000000 -r 3fbd172e4055 tool-data/vsnp_excel_filter.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/vsnp_excel_filter.loc.sample Mon Mar 09 13:42:19 2020 -0400 @@ -0,0 +1,4 @@ +## vSNP Excel Filter files +#Value Name Path Description +#AF2122 Mbovis_define_filter.xlsx vsnp/AF2122/Mbovis_remove_from_analysis.xlsx Excel filter file for Mycobacterium bovis AF2122/97 +#NC_006932 Bab1_define_filter.xlsx /vsnp/NC_006932/Bab1_remove_from_analysis.xlsx Excel filter file for Brucella abortus bv. 1 str. 9-941 diff -r 000000000000 -r 3fbd172e4055 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Mar 09 13:42:19 2020 -0400 @@ -0,0 +1,7 @@ + + + value, name, path, description + +
+
+