changeset 2:7d2252852f96 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55

--- a/data_manager/data_manager_sortmerna_download.py	Tue Jun 06 13:40:27 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.py	Tue Jun 13 12:03:08 2017 -0400
@@ -4,6 +4,7 @@
 import argparse
 import json
 import os
+import shutil
 import tarfile
 import requests
 import subprocess
@@ -126,23 +127,28 @@
         if not filename.endswith("fasta"):
             continue
         input_filepath = os.path.join(file_dir, filename)
-        output_filepath = os.path.join(target_dir, filename)
-        # Move file
-        os.rename(input_filepath, output_filepath)
+        # Extract the db name
+        db_name = os.path.splitext(filename)[0]
+        # Create the directory where to put the fasta files and indexed files
+        filedir = os.path.join(target_dir, db_name)
+        os.mkdir(filedir)
+        fasta_filepath = os.path.join(filedir, "%s.fasta" % db_name)
+        indexed_filepath = os.path.join(filedir, db_name)
+        # Move the fasta file
+        shutil.move(input_filepath, fasta_filepath)
         # Index the file with indexdb_rna
         command = "indexdb_rna --ref %s,%s" % (
-            output_filepath,
-            os.path.splitext(output_filepath)[0])
+            fasta_filepath,
+            indexed_filepath)
         process = subprocess.call(command, shell=True )
         # Add entry in the data table
-        db_name = os.path.splitext(filename)[0]
         add_data_table_entry(
             data_tables,
             "rRNA_databases",
             dict(
-                value=version,
+                value="%s-%s" %(version, db_name),
                 name=db_name,
-                path=output_filepath))
+                path=filedir))
 
 
 def download_db(data_tables, version, target_dir):

--- a/data_manager_conf.xml	Tue Jun 06 13:40:27 2017 -0400
+++ b/data_manager_conf.xml	Tue Jun 13 12:03:08 2017 -0400
@@ -6,11 +6,11 @@
                 <column name="value" />  <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="path" output_ref="out_file" >
-                    <move type="file">
+                    <move type="directory">
                         <source>${path}</source>
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}/${name}.fasta</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>