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view data_manager_conf.xml @ 2:6ad9205c1307

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Update to SnpEff version 3.3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:09:29 -0500
parents e1d9f6a0ad53
children
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<?xml version="1.0"?>
<data_managers>
  <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" >
    <data_table name="snpeff_databases">  <!-- Defines a Data Table to be modified. -->
      <output> <!-- Handle the output of the Data Manager Tool -->
        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
        <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
      </output>
    </data_table>
  </data_manager>
  <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" >
    <data_table name="snpeff_genomedb">  <!-- Defines a Data Table to be modified. -->
      <output> <!-- Handle the output of the Data Manager Tool -->
        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
        <column name="path" output_ref="out_file" >
          <move type="directory" relativize_symlinks="True">
            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/data</target>
          </move>
          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/data</value_translation>
          <value_translation type="function">abspath</value_translation>
        </column>
      </output>
    </data_table>
    <data_table name="snpeff_regulationdb">  <!-- Defines a Data Table to be modified. -->
      <output> <!-- Handle the output of the Data Manager Tool -->
        <column name="genome" /> <!-- 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="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
      </output>
    </data_table>
    <data_table name="snpeff_annotations">  <!-- Defines a Data Table to be modified. -->
      <output> <!-- Handle the output of the Data Manager Tool -->
        <column name="genome" /> <!-- 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="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
      </output>
    </data_table>
  </data_manager>
</data_managers>