<tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.5" profile="19.05">
    <requirements>
        <requirement type="package" version="377">ucsc-fatotwobit</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <description>builder</description>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/twobit_builder.py'
'${out_file}'
$long
--fasta_filename '${all_fasta_source.fields.path}'
--fasta_dbkey '${all_fasta_source.fields.dbkey}'
--fasta_description '${all_fasta_source.fields.name}'
    ]]></command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="sequence_name" type="text" value="" label="Name of sequence" />
        <param name="sequence_id" type="text" value="" label="ID for sequence" />
        <param argument="--long" type="boolean" truevalue="--long" falsevalue="" label="Use the -long option for very big genomes." />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <tests>
        <test>
            <param name="all_fasta_source" value="sacCer2"/>
            <param name="sequence_name" value=""/>
            <output name="out_file" file="data_manager_twobit.json"/>
        </test>
    </tests>

    <help>
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>