# HG changeset patch
# User sanbi-uwc
# Date 1457187561 18000
# Node ID d04a59b7684515ebb1471cd796b34a2d650b685c
# Parent  8dd4b25716d11548119f73a8c455814f691204a2
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 03f281362d5cf7c4d2a813203b83f5d12eb8ca46

diff -r 8dd4b25716d1 -r d04a59b76845 data_manager/novocraft_index_builder.py
--- a/data_manager/novocraft_index_builder.py	Sat Mar 05 07:55:06 2016 -0500
+++ b/data_manager/novocraft_index_builder.py	Sat Mar 05 09:19:21 2016 -0500
@@ -47,7 +47,8 @@
     #    fasta_filename,
     #    nslots)
     #cmdline = shlex.split(cmdline_str)
-    cmdline = ('touch', '{}/foo.nix'.format(target_directory))
+    index_filename = 'foo.nix'
+    cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
     try:
         check_call(cmdline)
     except CalledProcessError:
@@ -55,6 +56,7 @@
 
     data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory )
     _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+    return ( index_filename )
 
 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
@@ -78,7 +80,7 @@
 REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)
 
 def main():
-    parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this")
+    parser = argparse.ArgumentParser(description="Generate Novo-craft genome index and JSON describing this")
     parser.add_argument('output_filename')
     parser.add_argument('--dbkey_description')
     parser.add_argument('--data_table_name', default='novocraft_index')
diff -r 8dd4b25716d1 -r d04a59b76845 data_manager_conf.xml
--- a/data_manager_conf.xml	Sat Mar 05 07:55:06 2016 -0500
+++ b/data_manager_conf.xml	Sat Mar 05 09:19:21 2016 -0500
@@ -7,8 +7,10 @@
                 <column name="dbkey" />
                 <column name="name" />
                 <column name="path" output_ref="out_file">
-                    <move type="directory" relative_symlinks="True">
+                    <move type="file">
+                        <!--<move type="directory" relative_symlinks="True">-->
                         <!-- no need to set source, gets taken from out_dir.extra_files_path -->
+                         <source>${path}</source> <!-- File name within the extra files path -->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/novocraft_index/${value}</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/novocraft_index/${value}/${path}</value_translation>