# HG changeset patch
# User dfornika
# Date 1507756061 14400
# Node ID 0b3b4f9276b4dd2b078c27d4156318fe4ee22f47
# Parent  fd3c9d4c6c5a50fef751ce6a2f6f9cd171c75953
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty

diff -r fd3c9d4c6c5a -r 0b3b4f9276b4 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 16:57:28 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 17:07:41 2017 -0400
@@ -1,22 +1,26 @@
 #!/usr/bin/env python
+
 from __future__ import print_function
 
 import argparse
+import errno
 import os
+import string
 import subprocess
 import sys
-import errno
+
 from json import dumps, loads
-import string
+
 
 DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
 
 
 def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
-    database_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_k" + str(kmer_size) + "_pubmlst"
+    scheme_files_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_pubmlst"
+    database_path = scheme_files_path + "_k" + str(kmer_size)
     database_name = database_path + ".h5"
     display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)"
-    args = [ 'mentalist', 'download_pubmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', database_path]
+    args = [ 'mentalist', 'download_pubmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', scheme_files_path]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
     if return_code: