view macros.xml @ 0:8bbf903bf0cb draft

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<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.10.5">kraken</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code description="Tool exception" level="fatal" range="1:" />
        </stdio>
    </xml>
    <xml name="version_command">
        <version_command>export LC_ALL=C &amp;&amp; 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 databases are available built-in" type="no_options" />
            </options>
        </param>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
        </citations>
    </xml>
    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.path}/${kraken_database.fields.name}</token>
</macros>