# HG changeset patch
# User blankenberglab
# Date 1631278614 0
# Node ID aec9bc48cdb70ac8eb18b144f8b0b688681604b3
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
diff -r 000000000000 -r aec9bc48cdb7 data_manager/data_manager_refgenie_pull.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_refgenie_pull.py Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+
+import argparse
+import logging
+from base64 import urlsafe_b64encode
+from urllib.parse import urljoin
+
+import refgenconf
+import requests
+
+
+log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull")
+
+
+def galaxy_code_get_refgenie_assets(refgenie_config_file):
+ rgc = refgenconf.RefGenConf(refgenie_config_file)
+ rval = []
+ for urlname, genomes in rgc.listr().items():
+ urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8')
+ ul = []
+ for genome, assets in genomes.items():
+ al = []
+ for name in assets:
+ al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False})
+ ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False})
+ rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False})
+ return rval
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('-n', '--names', dest='names', action='store', default=None, help='Table names to reload')
+ parser.add_argument('-u', '--url', dest='url', action='store', default=None, help='Base url for reload')
+ parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key')
+
+ args = parser.parse_args()
+ if not args.names:
+ tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json()
+ args.names = [d.get('name') for d in tables]
+ for name in args.names:
+ print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json())
diff -r 000000000000 -r aec9bc48cdb7 data_manager/data_manager_refgenie_pull.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_refgenie_pull.xml Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,69 @@
+
+ from remote resource
+
+ macros.xml
+
+
+ refgenie
+
+
+
+
+
+ > '${out_log}' 2>&1
+ &&
+ #end for
+ echo '{}' > '${out_file}'
+ #if $api_refresh:
+ && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}' >> '${out_log}'
+ #end if
+ ]]>
+
+
+ .+/.+/.+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/gigascience/giz149
+ 10.1101/2020.10.09.327114
+
+
diff -r 000000000000 -r aec9bc48cdb7 data_manager/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,4 @@
+
+ 0.9.1
+
+
diff -r 000000000000 -r aec9bc48cdb7 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,5 @@
+
+
+
+
+
diff -r 000000000000 -r aec9bc48cdb7 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,3 @@
+
+
+
diff -r 000000000000 -r aec9bc48cdb7 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,3 @@
+
+
+