comparison data_manager_conf.xml @ 15:367b0d693b0c draft default tip

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14:3bb91cebec5c

<?xml version="1.0"?>
<data_managers>
    <data_manager tool_file="data_manager/add_ctat_ref_lib.xml" id="ctat_genome_ref_lib_data_manager"> 
        <data_table name="ctat_genome_ref_libs">
            <output>
                <column name="value" />
                    <!-- value is used to uniquely identify this entry in the table.
                    For now id is also the name of the environment variable that is used within tools to
                    access a CTAT Resource Library. 
                    FIX - Need to get rid of that and use command line params...
                    -->
                <column name="name" />
                    <!-- name is used as the selector in the pull down lists for items in this table.
                    -->
                <column name="path" />
                    <!-- path is the absolute path of the corresponding CTAT Genome Reference Library.
                    -->
                <!-- <column name="path" output_ref="out_file"> -->
                    <!-- It is typical to move the data file, but because our tool gets the destination
                    location from the user, we do not want to move the data from that location.
                    The full path of the CTAT Resource library is returned in location. 
                    So no need to change the value either.
                    -->
                    <!-- <move type="file" relativize_symlinks="False"> -->
                        <!--<source>${path}</source> -->
                        <!--<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ctat_genome_lib_build_dir</target> -->
                    <!--</move> -->
                    <!--
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ctat_genome_lib_build_dir
                    </value_translation>
                    -->
                    <!-- The location returned by the tool should already be an absolute path.
                    <value_translation type="function">abspath</value_translation>
                    -->
                <!--</column> -->
            </output>
        </data_table>
    </data_manager>
</data_managers>

15:367b0d693b0c

<?xml version="1.0"?>
<data_managers>
    <data_manager tool_file="data_manager/add_ctat_centrifuge_index.xml" id="ctat_centrifuge_index_data_manager"> 
        <data_table name="ctat_centrifuge_indexes">
            <output>
                <column name="value" />
                    <!-- value is used to uniquely identify this entry in the table.
                    -->
                <column name="name" />
                    <!-- name is used as the selector in the pull down lists for items in this table.
                    -->
                <column name="path" />
                    <!-- path is the absolute path of the directory containing the centrifuge index files.
                    -->
                <!-- Same as the Genome Reference Library, we create the Centrifuge Index files where we want them.
                -->
            </output>
        </data_table>
    </data_manager>
</data_managers>