annotate data_manager_conf.xml @ 6:847c9ef56a52 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 12dc2dbca65c1e2e1cb51c163daf0fa251d84d8e"

<?xml version="1.0"?>
<data_managers>

    <data_manager tool_file="data_manager/bowtie2_index_builder.xml" id="bowtie2_index_builder" version="2.2.6">
        <data_table name="bowtie2_indexes">
            <output>
                <column name="value" />
                <column name="dbkey" />
                <column name="name" />
                <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}">${dbkey}/bowtie2_index/${value}</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>

        <data_table name="tophat2_indexes">
            <output>
                <column name="value" />
                <column name="dbkey" />
                <column name="name" />
                <column name="path" output_ref="out_file" >
                    <!-- no move, always happens as part of bowtie2 and uses that path -->
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${value}/${path}</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
    </data_manager>

</data_managers>