# HG changeset patch
# User greg
# Date 1581345380 18000
# Node ID f1a7a3faaf3d584e7dfb5d4b4e3c29e1bbbbfaa8
Uploaded
diff -r 000000000000 -r f1a7a3faaf3d .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Mon Feb 10 09:36:20 2020 -0500
@@ -0,0 +1,10 @@
+name: data_manager_vsnp_genbank
+owner: greg
+description: Data manager to download vSNP analysis Genbank file
+homepage_url: https://github.com/USDA-VS/vSNP
+long_description: |
+ vSNP generates annotated SNP tables, this data manager installs the vSNP Genbank file.
+remote_repository_url: "https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/data_managers/vsnp_genbank"
+type: unrestricted
+categories:
+- Data Managers
diff -r 000000000000 -r f1a7a3faaf3d data_manager/vsnp_genbank_fetcher.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_genbank_fetcher.py Mon Feb 10 09:36:20 2020 -0500
@@ -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, 'w') 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'] = "Genbank file for %s" % name
+ data_manager_json["data_tables"]["vsnp_genbank"] = 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 Genbank 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 f1a7a3faaf3d data_manager/vsnp_genbank_fetcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_genbank_fetcher.xml Mon Feb 10 09:36:20 2020 -0500
@@ -0,0 +1,100 @@
+
+
+ Download vSNP Genbank files
+
+ python
+
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diff -r 000000000000 -r f1a7a3faaf3d data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Feb 10 09:36:20 2020 -0500
@@ -0,0 +1,21 @@
+
+
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diff -r 000000000000 -r f1a7a3faaf3d tool-data/vsnp_genbank.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/vsnp_genbank.loc.sample Mon Feb 10 09:36:20 2020 -0500
@@ -0,0 +1,4 @@
+## vSNP Genbank files
+#Value Name Path Description
+#AF2122 Mycobacterium_AF2122/NC_002945v4.gbk vsnp/AF2122/Mycobacterium_AF2122/NC_002945v4.gbk Genbank file for Mycobacterium bovis AF2122/97
+#NC_006932 Brucella_abortus1/NC_006932-NC_006933.gbk /vsnp/NC_006932/Brucella_abortus1/NC_006932-NC_006933.gbk Genbank file for Brucella abortus bv. 1 str. 9-941
diff -r 000000000000 -r f1a7a3faaf3d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Feb 10 09:36:20 2020 -0500
@@ -0,0 +1,7 @@
+
+
+ value, name, path, description
+
+
+
+