Mercurial > repos > jjohnson > defuse
changeset 20:b649c729be4c
Change tool data table to defuse_reference
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 24 Jun 2013 07:01:48 -0500 |
| parents | 1af6f32ff592 |
| children | 1bc79c9d6165 |
| files | data_manager_conf.xml datamanager_create_reference.py tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 12 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager_conf.xml Fri Jun 21 14:46:11 2013 -0500 +++ b/data_manager_conf.xml Mon Jun 24 07:01:48 2013 -0500 @@ -3,10 +3,10 @@ <data_manager tool_file="datamanager_create_reference.xml" id="data_manager_defuse_reference" > <data_table name="defuse_reference"> <!-- Defines a Data Table to be modified. --> <output> <!-- Handle the output of the Data Manager Tool --> - <column name="unique_id" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> <column name="dbkey" /> <column name="name" /> - <column name="config" output_ref="out_file" > <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" --> + <column name="path" output_ref="out_file" > <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" --> <move type="directory"> <!-- Moving a file from the extra files path of "out_file" --> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/defuse</target> <!-- Target Location to store the file, directories are created as needed --> </move>
--- a/datamanager_create_reference.py Fri Jun 21 14:46:11 2013 -0500 +++ b/datamanager_create_reference.py Mon Jun 24 07:01:48 2013 -0500 @@ -83,12 +83,12 @@ except Exception, e: stop_err( 'Error creating defuse reference:\n' + str( e ) ) config_dict = get_config_dict(config, dataset_directory=target_directory) - data_table_entry = dict(unique_id=dbkey, dbkey=dbkey, name=description, path=config_name) + data_table_entry = dict(value=dbkey, dbkey=dbkey, name=description, path=config_name) _add_data_table_entry( data_manager_dict, data_table_entry ) def _add_data_table_entry( data_manager_dict, data_table_entry ): data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables']['defuse'] = data_manager_dict['data_tables'].get( 'defuse', [] ) - data_manager_dict['data_tables']['defuse'].append( data_table_entry ) + data_manager_dict['data_tables']['defuse_reference'] = data_manager_dict['data_tables'].get( 'defuse_reference', [] ) + data_manager_dict['data_tables']['defuse_reference'].append( data_table_entry ) return data_manager_dict def main():
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jun 24 07:01:48 2013 -0500 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="defuse_reference" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/defuse_reference.loc" /> + </table> +</tables>