view macros.xml @ 5:bc3e90fd13be draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3873b52450c86190e4fb8767cffe5730d6e37692"

<?xml version="1.0"?>
<macros>
    <token name="@WRAPPER_VERSION@">1.3.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.1.1">kraken</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[
            export LC_ALL=C && kraken --version
        ]]></version_command>
    </xml>
    <xml name="input_database">
        <param label="Select a Kraken database" name="kraken_database" type="select">
            <options from_data_table="kraken_databases">
                <validator message="No Kraken database is available" type="no_options" />
            </options>
        </param>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
        </citations>
    </xml>
    <!-- See the kraken_databases.loc.sample documentation,
         this if statement is for backward compatibility as early
         versions of the wrapper assumed the UI facing field name
         was also part of the directory path -->
    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
    <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
</macros>