# HG changeset patch
# User bebatut
# Date 1497276324 14400
# Node ID afe988ad1e1deecea29b288ccdaeb3bef7ef10bd
# Parent  240907f60646503da538ee8d640f07de05e40c95
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit d10a3522c8a776162c5f3936c5e820bb3fa5c3ca-dirty

diff -r 240907f60646 -r afe988ad1e1d data_manager/data_manager_sortmerna_download.py
--- a/data_manager/data_manager_sortmerna_download.py	Mon Jun 12 09:35:57 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.py	Mon Jun 12 10:05:24 2017 -0400
@@ -126,17 +126,19 @@
         if not filename.endswith("fasta"):
             continue
         input_filepath = os.path.join(file_dir, filename)
-        output_filepath = os.path.join(target_dir, filename)
+        output_dir = os.path.join(target_dir, filename)
+        os.makedir(output_dir)
+        db_name = os.path.splitext(filename)[0]
+        fasta_filepath = os.path.join(output_dir, "%s.fasta" % db_name)
+        indexed_filepath = os.path.join(output_dir, db_name)
         # Move file
-        os.rename(input_filepath, output_filepath)
+        os.rename(input_filepath, fasta_filepath)
         # Index the file with indexdb_rna
-        indexed_filepath = os.path.splitext(output_filepath)[0]
         command = "indexdb_rna --ref %s,%s" % (
-            output_filepath,
+            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",
diff -r 240907f60646 -r afe988ad1e1d data_manager/data_manager_sortmerna_download.xml
--- a/data_manager/data_manager_sortmerna_download.xml	Mon Jun 12 09:35:57 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.xml	Mon Jun 12 10:05:24 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.1" tool_type="manage_data">
+<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.2" tool_type="manage_data">
     <description>reference databases</description>
     <macros>
         <import>macros.xml</import>
diff -r 240907f60646 -r afe988ad1e1d data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Jun 12 09:35:57 2017 -0400
+++ b/data_manager_conf.xml	Mon Jun 12 10:05:24 2017 -0400
@@ -6,27 +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">
-                        <source>${path}.fasta</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.fasta</target>
-                    </move>
-                    <move type="file">
-                        <source>${path}.stats</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.stats</target>
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}</target>
                     </move>
-                    <move type="file">
-                        <source>${path}.pos_0.dat</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.pos_0.dat</target>
-                    </move>
-                    <move type="file">
-                        <source>${path}.kmer_0.dat</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.kmer_0.dat</target>
-                    </move>
-                    <move type="file">
-                        <source>${path}.bursttrie_0.dat</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}.bursttrie_0.dat</target>
-                    </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}.fasta</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>