view macros.xml @ 4:9709eedcff4b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6

<?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 ${kraken_database.fields.name}</token>
    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
</macros>