# HG changeset patch
# User dfornika
# Date 1516998885 18000
# Node ID c5658160ee70ef45e02ce99f97dd3f415ece4681
# Parent 038558f760a0eb8db8f08e8f314852fdc4c2d9db
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 30248a394608817fed641abc21dff2fbf6283eb7
diff -r 038558f760a0 -r c5658160ee70 data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml Tue Dec 05 13:55:37 2017 -0500
+++ b/data_managers/data_manager_conf.xml Fri Jan 26 15:34:45 2018 -0500
@@ -45,4 +45,19 @@
+
+
+
+
+
diff -r 038558f760a0 -r c5658160ee70 data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py Fri Jan 26 15:34:45 2018 -0500
@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import errno
+import os
+import string
+import subprocess
+import sys
+
+from json import dumps, loads
+
+
+DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
+
+
+def mentalist_download_enterobase( data_manager_dict, kmer_size, scheme, type, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+ translation_table = string.maketrans(string.punctuation, ("_" * 32))
+ base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_enterobase"
+ today = datetime.date.today().isoformat()
+ scheme_files_path = base_path + "_scheme_" + today
+ database_path = base_path + "_k" + str(kmer_size) + "_" + today
+ database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld"
+ display_name = scheme + " k=" + str(kmer_size) + " (Enterobase) " + today
+ args = [ 'mentalist', 'download_enterobase', '-s', scheme, '-t', type, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path]
+ proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+ return_code = proc.wait()
+ if return_code:
+ print("Error building database.", file=sys.stderr)
+ sys.exit( return_code )
+ data_table_entry = dict( value=database_path, dbkey='PubMLST', name=display_name, path=database_name )
+ for data_table_name in data_table_names:
+ _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+
+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
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('params')
+ parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help="Scheme: ('E'=Escherichia/Shigella, 'S'=Salmonella, 'Y'=Yersinia)")
+ parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
+ parser.add_argument( '-t', '--type', dest='type', default=None, help="Type: ('cg'=cgMLST, 'wg'=wgMLST')")
+ args = parser.parse_args()
+
+ params = loads( open( args.params ).read() )
+ target_directory = params[ 'output_data' ][0]['extra_files_path']
+
+ try:
+ os.mkdir( target_directory )
+ except OSError as exc:
+ if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+ pass
+ else:
+ raise
+
+ data_manager_dict = {}
+
+ # build the index
+ mentalist_download_enterobase( data_manager_dict, args.kmer_size, args.scheme, args.type, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
+
+ # save info to json file
+ open( args.params, 'wb' ).write( dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+ main()
diff -r 038558f760a0 -r c5658160ee70 data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml Fri Jan 26 15:34:45 2018 -0500
@@ -0,0 +1,35 @@
+
+
+
+ mentalist
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1101/172858
+
+
diff -r 038558f760a0 -r c5658160ee70 data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_enterobase/tool_data_table_conf.xml.sample Fri Jan 26 15:34:45 2018 -0500
@@ -0,0 +1,8 @@
+
+
+
+
+
\ No newline at end of file