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comparison data_manager_conf.xml @ 5:78bcf4ac437c

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Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
author Jim Johnson <jj@umn.edu>
date Tue, 13 Jan 2015 12:54:20 -0600
parents 6a378d0f4856
children
comparison
equal deleted inserted replaced
4:6a378d0f4856 5:78bcf4ac437c
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_snpeff4_databases" > 3 <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" >
4 <data_table name="snpeff4_databases"> <!-- Defines a Data Table to be modified. --> 4 <data_table name="snpeffv_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="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
7 <column name="version" /> <!-- 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 --> 8 <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 --> 9 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
8 </output> 10 </output>
9 </data_table> 11 </data_table>
10 </data_manager> 12 </data_manager>
11 <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff4_download" > 13 <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" >
12 <data_table name="snpeff4_genomedb"> <!-- Defines a Data Table to be modified. --> 14 <data_table name="snpeffv_genomedb"> <!-- Defines a Data Table to be modified. -->
13 <output> <!-- Handle the output of the Data Manager Tool --> 15 <output> <!-- Handle the output of the Data Manager Tool -->
16 <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
17 <column name="version" /> <!-- 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 --> 18 <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 --> 19 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
16 <column name="path" output_ref="out_file" > 20 <column name="path" output_ref="out_file" >
17 <move type="directory" relativize_symlinks="True"> 21 <move type="directory" relativize_symlinks="True">
18 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4/data</target> 22 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4_0/data</target>
19 </move> 23 </move>
20 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4/data</value_translation> 24 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4_0/data</value_translation>
21 <value_translation type="function">abspath</value_translation> 25 <value_translation type="function">abspath</value_translation>
22 </column> 26 </column>
23 </output> 27 </output>
24 </data_table> 28 </data_table>
25 <data_table name="snpeff4_regulationdb"> <!-- Defines a Data Table to be modified. --> 29 <data_table name="snpeffv_regulationdb"> <!-- Defines a Data Table to be modified. -->
26 <output> <!-- Handle the output of the Data Manager Tool --> 30 <output> <!-- Handle the output of the Data Manager Tool -->
31 <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
32 <column name="version" /> <!-- 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 --> 33 <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 --> 34 <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 --> 35 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
30 </output> 36 </output>
31 </data_table> 37 </data_table>
32 <data_table name="snpeff4_annotations"> <!-- Defines a Data Table to be modified. --> 38 <data_table name="snpeffv_annotations"> <!-- Defines a Data Table to be modified. -->
33 <output> <!-- Handle the output of the Data Manager Tool --> 39 <output> <!-- Handle the output of the Data Manager Tool -->
40 <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
41 <column name="version" /> <!-- 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 --> 42 <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 --> 43 <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 --> 44 <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
37 </output> 45 </output>
38 </data_table> 46 </data_table>