# HG changeset patch
# User dfornika
# Date 1507835983 14400
# Node ID e038a8823a9994b553fa3cf358aa3e61eb341146
# Parent  d151478ebf9785261e9b0813a4f8ad10b22d1933
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty

diff -r d151478ebf97 -r e038a8823a99 data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml	Thu Oct 12 13:40:07 2017 -0400
+++ b/data_managers/data_manager_conf.xml	Thu Oct 12 15:19:43 2017 -0400
@@ -9,7 +9,7 @@
           <move type="directory" relativize_symlinks="True">
             <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
@@ -24,7 +24,7 @@
           <move type="directory" relativize_symlinks="True">
             <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
@@ -39,7 +39,7 @@
           <move type="directory" relativize_symlinks="True">
             <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
diff -r d151478ebf97 -r e038a8823a99 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	Thu Oct 12 13:40:07 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py	Thu Oct 12 15:19:43 2017 -0400
@@ -16,17 +16,19 @@
 
 
 def mentalist_download_cgmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
-    scheme_files_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_cgmlst"
-    database_path = scheme_files_path + "_k" + str(kmer_size)
-    database_name = database_path + ".h5"
-    display_name = scheme + " k=" + str(kmer_size) + " (cgMLST)"
-    args = [ 'mentalist', 'download_cgmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', scheme_files_path]
+    translation_table = string.maketrans(string.punctuation, ("_" * 32))
+    base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_cgmlst"
+    scheme_files_path = base_path + "_scheme"
+    database_path = base_path + "_k" + str(kmer_size)
+    database_name = base_path + "_k" + str(kmer_size) + ".h5"
+    display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)"
+    args = [ 'mentalist', 'download_cgmlst', '-s', scheme, '-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_name, dbkey='cgMLST', name=display_name, path=(database_path + "/" + database_name) )
+    data_table_entry = dict( value=database_path, dbkey='cgMLST', 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 )
 
diff -r d151478ebf97 -r e038a8823a99 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	Thu Oct 12 13:40:07 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Thu Oct 12 15:19:43 2017 -0400
@@ -28,7 +28,7 @@
     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_path + "/" + database_name) )
+    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 )