# HG changeset patch
# User dfornika
# Date 1554320844 14400
# Node ID 31686a3c30182f6e96a9873f2a8cbe37a7f15bdb
# Parent  7a90f3b437bfdb784468bc87db7b444878eb66c5
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/mentalist_v0.1/galaxy commit 3510ff53b3c1cc42940733dfaa7036673c0cea2a

diff -r 7a90f3b437bf -r 31686a3c3018 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Tue Jun 26 13:27:00 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Apr 03 15:47:24 2019 -0400
@@ -20,6 +20,8 @@
       <option value="Clostridioides difficile">Clostridioides difficile</option>
       <option value="Enterococcus faecium">Enterococcus faecium</option>
       <option value="Francisella tularensis">Francisella tularensis</option>
+      <option value="Klebsiella pneumoniae/variicola/quasipneumoniae">Klebsiella pneumoniae/variicola/quasipneumoniae</option>
+      <option value="Mycobacterium tuberculosis/bovis/africanum/canettii">Mycobacterium tuberculosis/bovis/africanum/canettii</option>
       <option value="Legionella pneumophila">Legionella pneumophila</option>
       <option value="Listeria monocytogenes">Listeria monocytogenes</option>
       <option value="Staphylococcus aureus">Staphylococcus aureus</option>
diff -r 7a90f3b437bf -r 31686a3c3018 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	Tue Jun 26 13:27:00 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Apr 03 15:47:24 2019 -0400
@@ -17,6 +17,7 @@
 
 
 def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+    scheme = scheme.replace('__pd__','#')
     translation_table = string.maketrans(string.punctuation, ("_" * 32))
     base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_pubmlst"
     today = datetime.date.today().isoformat()