Mercurial > repos > iuc > data_manager_build_bracken_database

comparison data_manager_conf.xml @ 6:a0f18c07696a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
author iuc
date Wed, 05 Nov 2025 13:31:43 +0000
parents 5bc823e95ed3
children
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5:cef566388a0f 6:a0f18c07696a
2 <data_manager tool_file="data_manager/bracken_build_database.xml" id="bracken_build_database"> 2 <data_manager tool_file="data_manager/bracken_build_database.xml" id="bracken_build_database">
3 <data_table name="bracken_databases"> 3 <data_table name="bracken_databases">
4 <output> 4 <output>
5 <column name="value"/> 5 <column name="value"/>
6 <column name="name"/> 6 <column name="name"/>
7 <column name="path" output_ref="out_file"/> 7 <column name="path" output_ref="out_file">
8 <move type="directory" relativize_symlinks="True">
9 <!-- we move the top level folder, since the path points to the bracken DB file -->
10 <source>
11 #import os
12 #set base_dir = os.path.dirname($path)
13 ${base_dir}
14 </source>
15 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${value}</target>
16 </move>
17 <!-- we store the path to the bracken DB file, since this is what bracken uses -->
18 <value_translation>
19 #import os
20 ${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${value}/${os.path.basename($path)}
21 </value_translation>
22 <value_translation type="function">abspath</value_translation>
23 </column>
8 </output> 24 </output>
25
9 </data_table> 26 </data_table>
10 </data_manager> 27 </data_manager>
11 </data_managers> 28 </data_managers>