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comparison data_manager_conf.xml @ 3:c6769a700e55

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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
comparison
equal deleted inserted replaced
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>