# HG changeset patch
# User dfornika
# Date 1507759286 14400
# Node ID 9a90295d0dfbcc74dd4e4158f623c7481f93c903
# Parent  c3cef07b5132ea724064fe1cc615864f827d2c45
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty

diff -r c3cef07b5132 -r 9a90295d0dfb data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py	Wed Oct 11 17:49:06 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py	Wed Oct 11 18:01:26 2017 -0400
@@ -26,7 +26,7 @@
     if return_code:
         print("Error building database.", file=sys.stderr)
         sys.exit( return_code )
-    data_table_entry = dict( value=database_name, dbkey='cgMLST', name=display_name, path=database_path )
+    data_table_entry = dict( value=database_name, dbkey='cgMLST', name=display_name, path=(database_path + "/" + database_name) )
     for data_table_name in data_table_names:
         _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
 
diff -r c3cef07b5132 -r 9a90295d0dfb 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 17:49:06 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 18:01:26 2017 -0400
@@ -26,7 +26,7 @@
     if return_code:
         print("Error building database.", file=sys.stderr)
         sys.exit( return_code )
-    data_table_entry = dict( value=database_name, dbkey='PubMLST', name=display_name, path=database_path )
+    data_table_entry = dict( value=database_name, dbkey='PubMLST', name=display_name, path=(database_path + "/" + database_name) )
     for data_table_name in data_table_names:
         _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
 
diff -r c3cef07b5132 -r 9a90295d0dfb tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Wed Oct 11 17:49:06 2017 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Wed Oct 11 18:01:26 2017 -0400
@@ -7,7 +7,7 @@
     call
     -o '$output_file'
     -s '$sample_name'
-    --db '$kmer_db.fields.path'/'$kmer_db.fields.value'
+    --db '$kmer_db.fields.path'
     #if $discard_threshold
         -t '$discard_threshold'
     #end if