# HG changeset patch
# User sanbi-uwc
# Date 1536676778 14400
# Node ID f86c65c60056c5479ad28cdf02bf005c26f40bc8
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
diff -r 000000000000 -r f86c65c60056 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Tue Sep 11 10:39:38 2018 -0400
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 pvanheus
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff -r 000000000000 -r f86c65c60056 data_manager/shapeit_ref.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/shapeit_ref.py Tue Sep 11 10:39:38 2018 -0400
@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+
+from __future__ import division, print_function
+import argparse
+import json
+import os
+import os.path
+
+
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+ data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+ data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
+ data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
+ return data_manager_dict
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data')
+ parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
+ parser.add_argument('description', help='Description of reference set')
+ parser.add_argument('path', help='Filesystem path to directory containing this reference set')
+ parser.add_argument('prefix', help='Filename prefix for files in this reference set')
+ parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
+ args = parser.parse_args()
+
+ if not os.path.exists(args.path):
+ exit("Unable to find specified path {}".format(args.path))
+
+ prefix_exists = False
+ for filename in os.listdir(args.path):
+ if filename.startswith(args.prefix):
+ prefix_exists = True
+ break
+ else:
+ if not prefix_exists:
+ exit("Unable to find a file with prefix {} in {}".format(args.prefix, args.path))
+
+ for column in ('key', 'description', 'path', 'prefix'):
+ value = getattr(args, column)
+ if '\t' in value:
+ exit("TAB character found in {} argument".format(column))
+
+ data_manager_dict = {}
+ data_table_entry = dict(key=args.key, description=args.description, path=args.path, prefix=args.prefix)
+ _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
+
+ args.output_file.write(json.dumps(data_manager_dict) + '\n')
diff -r 000000000000 -r f86c65c60056 data_manager/shapeit_ref.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/shapeit_ref.xml Tue Sep 11 10:39:38 2018 -0400
@@ -0,0 +1,30 @@
+
+ >
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/nmeth.1785
+
+
\ No newline at end of file
diff -r 000000000000 -r f86c65c60056 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Sep 11 10:39:38 2018 -0400
@@ -0,0 +1,13 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r f86c65c60056 tool-data/shapeit_ref.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/shapeit_ref.loc.sample Tue Sep 11 10:39:38 2018 -0400
@@ -0,0 +1,7 @@
+#This file lists the locations of SHAPEIT reference data connections
+#
+#
+#
+#For example
+#
+#1000G_Phase3 1000 Genomes project haplotypes /path/to/shapeit_ref/1000G 1000GP_Phase3_
diff -r 000000000000 -r f86c65c60056 tool_data_tables_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_tables_conf.xml.sample Tue Sep 11 10:39:38 2018 -0400
@@ -0,0 +1,7 @@
+
+
+
+ key, description, path, prefix
+
+
+
\ No newline at end of file