view macros.xml @ 0:a77e88d426d9 draft

planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty

<macros>
    <token name="@TOOL_VERSION@">2.0.7_beta</token>
    <token name="@INTYPES@">
        fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz
    </token>
    <xml name="input_database">
        <param label="Select a Kraken2 database" name="kraken2_database" type="select">
            <options from_data_table="kraken2_databases">
                <validator message="No Kraken2 database is available" type="no_options" />
            </options>
        </param>
    </xml>
    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken2_database.fields.path}/${kraken2_database.fields.name}' ]; then export KRAKEN2_DEFAULT_DB='${kraken2_database.fields.path}/${kraken2_database.fields.name}'; else export KRAKEN2_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
    <token name="@INPUT_DATABASE@">--db "\$KRAKEN2_DEFAULT_DB"</token>
</macros>