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Add abspath value translation to data_manager_conf.xml.
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 04 Jun 2013 14:57:33 -0400
parents 2c5dc42b31b6
children
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<?xml version="1.0"?>
<data_managers>
    
    <data_manager tool_file="data_manager/data_manager_sam_fa_index_builder.xml" id="sam_fa_index_builder" version="0.0.1">
        <data_table name="sam_fa_indexes">
            <output>
                <column name="line_type" />
                <column name="value" />
                <column name="path" output_ref="out_file" >
                    <move type="directory" relativize_symlinks="True">
                        <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/sam_index/${value}</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/sam_index/${value}/${path}</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
    </data_manager>
    
</data_managers>