<tool id="bwa_mem2_idx" name="BWA-MEM2 indexer"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
    <description>Build BWA-MEM2 reference index</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
mkdir '$index.extra_files_path' &&
cd '$index.extra_files_path' &&
bwa-mem2 index -p 'reference' '${reference}'
    ]]></command>
    <inputs>
        <param name="reference" type="data" format="fasta,fasta.gz" label="Select a genome to index" help="Build an index for this FASTA sequence."/>
    </inputs>
    <outputs>
        <data name="index" format="bwa_mem2_index"/>
    </outputs>
    <tests>
        <test>
            <param name="reference" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <output name="index" ftype="bwa_mem2_index">
                <extra_files name="reference.0123" type="file" value="test-cache/reference.0123"></extra_files>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What is does**
BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.

This tools build a reference index for the bwa-mem2 galaxy tool.

@info@
    ]]></help>
    <expand macro="citations" />
</tool>