<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.1" profile="23.0">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="3.8.3">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/bowtie_index_builder.py'
'${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 name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
        <param name="sequence_id" type="text" 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><![CDATA[
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    ]]></help>
    <citations>
        <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
    </citations>
</tool>