Mercurial > repos > dfornika > mentalist

changeset 20:3738f0bc436b draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty
author dfornika
date Wed, 11 Oct 2017 20:15:41 -0400
parents 9a90295d0dfb
children aaafd968651a
files data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py
diffstat 2 files changed, 13 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Wed Oct 11 18:01:26 2017 -0400
+++ b/data_managers/data_manager_conf.xml	Wed Oct 11 20:15:41 2017 -0400
@@ -7,9 +7,9 @@
         <column name="name" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>
+            <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}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
@@ -22,9 +22,9 @@
         <column name="name" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>
+            <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}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
@@ -38,9 +38,9 @@
 	<column name="dbkey" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>
+            <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}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 18:01:26 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 20:15:41 2017 -0400
@@ -16,17 +16,18 @@
 
 
 def mentalist_download_pubmlst( 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) + "_pubmlst"
-    database_path = scheme_files_path + "_k" + str(kmer_size)
-    database_name = database_path + ".h5"
+    base_path = scheme.lower().replace(" ", "_").translate("_", string.punctuation) + "_pubmlst"
+    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_pubmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', scheme_files_path]
+    args = [ 'mentalist', 'download_pubmlst', '-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='PubMLST', name=display_name, path=(database_path + "/" + database_name) )
+    data_table_entry = dict( value=database_path, 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 )
 
@@ -41,8 +42,8 @@
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('params')
+    parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help='Scheme' )
     parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
-    parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help='Scheme' )
     args = parser.parse_args()
 
     params = loads( open( args.params ).read() )