Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
changeset 7:d04a59b76845 draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 03f281362d5cf7c4d2a813203b83f5d12eb8ca46
| author | sanbi-uwc |
|---|---|
| date | Sat, 05 Mar 2016 09:19:21 -0500 |
| parents | 8dd4b25716d1 |
| children | 56e8324519c4 |
| files | data_manager/novocraft_index_builder.py data_manager_conf.xml |
| diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- 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')
--- 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>