Mercurial > repos > jjohnson > data_manager_snpeff
comparison data_manager_conf.xml @ 3:c6769a700e55
Update loc data to separate version 4 databases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 21 Oct 2014 14:04:33 -0500 |
| parents | bc50aa3b328a |
| children | 6a378d0f4856 |
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| 2:5a01e5cfa6bc | 3:c6769a700e55 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <data_managers> | 2 <data_managers> |
| 3 <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" > | 3 <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" > |
| 4 <data_table name="snpeff_databases"> <!-- Defines a Data Table to be modified. --> | 4 <data_table name="snpeff4_databases"> <!-- Defines a Data Table to be modified. --> |
| 5 <output> <!-- Handle the output of the Data Manager Tool --> | 5 <output> <!-- Handle the output of the Data Manager Tool --> |
| 6 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 6 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 7 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 7 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 8 </output> | 8 </output> |
| 9 </data_table> | 9 </data_table> |
| 10 </data_manager> | 10 </data_manager> |
| 11 <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" > | 11 <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" > |
| 12 <data_table name="snpeff_genomedb"> <!-- Defines a Data Table to be modified. --> | 12 <data_table name="snpeff4_genomedb"> <!-- Defines a Data Table to be modified. --> |
| 13 <output> <!-- Handle the output of the Data Manager Tool --> | 13 <output> <!-- Handle the output of the Data Manager Tool --> |
| 14 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 14 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 15 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 15 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 16 <column name="path" output_ref="out_file" > | 16 <column name="path" output_ref="out_file" > |
| 17 <move type="directory" relativize_symlinks="True"> | 17 <move type="directory" relativize_symlinks="True"> |
| 18 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/data</target> | 18 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4/data</target> |
| 19 </move> | 19 </move> |
| 20 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/data</value_translation> | 20 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4/data</value_translation> |
| 21 <value_translation type="function">abspath</value_translation> | 21 <value_translation type="function">abspath</value_translation> |
| 22 </column> | 22 </column> |
| 23 </output> | 23 </output> |
| 24 </data_table> | 24 </data_table> |
| 25 <data_table name="snpeff_regulationdb"> <!-- Defines a Data Table to be modified. --> | 25 <data_table name="snpeff4_regulationdb"> <!-- Defines a Data Table to be modified. --> |
| 26 <output> <!-- Handle the output of the Data Manager Tool --> | 26 <output> <!-- Handle the output of the Data Manager Tool --> |
| 27 <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 27 <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 28 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 28 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 29 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 29 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 30 </output> | 30 </output> |
| 31 </data_table> | 31 </data_table> |
| 32 <data_table name="snpeff_annotations"> <!-- Defines a Data Table to be modified. --> | 32 <data_table name="snpeff4_annotations"> <!-- Defines a Data Table to be modified. --> |
| 33 <output> <!-- Handle the output of the Data Manager Tool --> | 33 <output> <!-- Handle the output of the Data Manager Tool --> |
| 34 <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 34 <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 35 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 35 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 36 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> | 36 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> |
| 37 </output> | 37 </output> |