# HG changeset patch
# User greg
# Date 1581098545 18000
# Node ID 84a356e0950a6e23c1a5d767f987356911562f25
Uploaded
diff -r 000000000000 -r 84a356e0950a .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Fri Feb 07 13:02:25 2020 -0500
@@ -0,0 +1,10 @@
+name: data_manager_vsnp_excel
+owner: greg
+description: Data manager to download vSNP analysis Excel file
+homepage_url: https://github.com/USDA-VS/vSNP
+long_description: |
+ vSNP generates annotated SNP tables, this data manager installs the vSNP Excel file.
+remote_repository_url: "https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/data_managers/vsnp_excel"
+type: unrestricted
+categories:
+- Data Managers
diff -r 000000000000 -r 84a356e0950a data_manager/vsnp_excel_fetcher.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_excel_fetcher.py Fri Feb 07 13:02:25 2020 -0500
@@ -0,0 +1,64 @@
+import argparse
+import json
+import os
+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, target_directory):
+ file_path = os.path.abspath(os.path.join(target_directory, 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
+ finally:
+ if src:
+ src.close()
+ return file_path
+
+
+def download(dbkey, display_name, url, out_file):
+
+ with open(out_file) as fh:
+ params = json.loads(fh.read())
+
+ work_directory = params['output_data'][0]['extra_files_path']
+ target_directory = os.path.abspath(os.path.join(work_directory, "vsnp", dbkey))
+ os.mkdir(target_directory)
+ file_path = url_download(url, target_directory)
+ entry_name = "%s" % 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 file for %s" % display_name
+ data_manager_json["data_tables"]["vsnp_excel"] = 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('--display_name', dest='display_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.display_name, args.url, args.out_file)
diff -r 000000000000 -r 84a356e0950a data_manager/vsnp_excel_fetcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_excel_fetcher.xml Fri Feb 07 13:02:25 2020 -0500
@@ -0,0 +1,132 @@
+
+
+ Download reference databases
+
+ python
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diff -r 000000000000 -r 84a356e0950a data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Feb 07 13:02:25 2020 -0500
@@ -0,0 +1,19 @@
+
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diff -r 000000000000 -r 84a356e0950a tool-data/vsnp_excel.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/vsnp_excel.loc.sample Fri Feb 07 13:02:25 2020 -0500
@@ -0,0 +1,4 @@
+## vSNP Excel files
+#Value Name Path Description
+#AF2122 Mbovis_define_filter.xlsx vsnp/AF2122/Mbovis_define_filter.xlsx Excel file for Mycobacterium bovis AF2122/97
+#NC_006932 Bab1_define_filter.xlsx /vsnp/NC_006932/Bab1_define_filter.xlsx Excel file for Brucella abortus bv. 1 str. 9-941
diff -r 000000000000 -r 84a356e0950a tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Feb 07 13:02:25 2020 -0500
@@ -0,0 +1,7 @@
+
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+ value, name, path, description
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+