<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="0.0.1">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="1.0.0">bowtie</requirement>
    </requirements>
    <command interpreter="python">bowtie_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bowtie_indexes"</command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param type="text" name="sequence_name" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id "/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <help>

.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically. 

    </help>
</tool>