view data_manager/mitos_fetcher.xml @ 0:d1beb6fba192 draft default tip

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit a7354d02377105590891f7337f472dc2a2f224a4

<?xml version="1.0"?>
<tool id="mitos_fetcher_data_manager" name="MITOS" tool_type="manage_data" version="0.0.1">
    <description>reference data downloader</description>
    <command detect_errors="exit_code">
    <![CDATA[
    python '$__tool_directory__/data_manager.py' 
    --out '${out_file}'
    --type '$type_cond.type_select'
    --db '$type_cond.database'
    ]]>
    </command>
    <inputs>
        <conditional name="type_cond">
            <param name="type_select" type="select" label="MITOS version">
                <option value="mitos">MITOS</option>
                <option value="mitos2">MITOS2</option>
	    </param>
            <when value="mitos">
                <param name="database" type="select" label="Refernce data version">
                    <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
                </param>
            </when>
            <when value="mitos2">
                <param name="database" type="select" label="Refernce data version">
                    <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
                    <option value="refseq63m">RefSeq63 Metazoa</option>
                    <option value="refseq63f">RefSeq63 Fungi</option>
                    <option value="refseq63o">RefSeq63 Opisthokonta</option>
                    <option value="refseq81m">RefSeq81 Metazoa</option>
                    <option value="refseq81f">RefSeq81 Fungi</option>
                    <option value="refseq81o">RefSeq81 Opisthokonta</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <conditional name="type_cond">
                <param name="type_select" value="mitos"/>
                <param name="database" value="mitos1-refdata"/>
            </conditional>
            <output name="out_file" file="mitos_refseq39.json"/>
        </test>
    </tests>
    <help>
TODO
    </help>
</tool>