# HG changeset patch
# User bebatut
# Date 1497271306 14400
# Node ID 3c14e5982438767de873a5d55ba36aead3697fc4
# Parent  bbbcaf67e9fc1fdafc5005aac1dd24d906a0e902
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty

diff -r bbbcaf67e9fc -r 3c14e5982438 data_manager/data_manager_sortmerna_download.py
--- a/data_manager/data_manager_sortmerna_download.py	Mon Jun 12 08:06:07 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.py	Mon Jun 12 08:41:46 2017 -0400
@@ -130,9 +130,10 @@
         # Move file
         os.rename(input_filepath, output_filepath)
         # Index the file with indexdb_rna
+        indexed_filepath = os.path.splitext(output_filepath)[0]
         command = "indexdb_rna --ref %s,%s" % (
             output_filepath,
-            os.path.splitext(output_filepath)[0])
+            indexed_filepath)
         process = subprocess.call(command, shell=True )
         # Add entry in the data table
         db_name = os.path.splitext(filename)[0]
@@ -142,7 +143,7 @@
             dict(
                 value="%s-%s" %(version, db_name),
                 name=db_name,
-                path=output_filepath))
+                path=indexed_filepath))
 
 
 def download_db(data_tables, version, target_dir):
diff -r bbbcaf67e9fc -r 3c14e5982438 data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Jun 12 08:06:07 2017 -0400
+++ b/data_manager_conf.xml	Mon Jun 12 08:41:46 2017 -0400
@@ -8,6 +8,10 @@
                 <column name="path" output_ref="out_file" >
                     <move type="file">
                         <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}</target>
+                    </move>
+                    <move type="file">
+                        <source>${path}.fasta</source>
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.fasta</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}.fasta</value_translation>