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<tool id="bwa_index_builder_data_manager" name="BWA index" tool_type="manage_data" version="0.0.1">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="0.5.9">bwa</requirement>
    </requirements>
    <command interpreter="python">bwa_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 "bwa_indexes"</command>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <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" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" />
        
        <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index">
            <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option>
            <option value="is" hel="Small genomes">IS linear-time algorithm</option>
            <!-- <option value="div">div</option> -->
            <option value="bwtsw" help="Large genomes">BWT-SW</option>
        </param>
        
    </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>