<tool id="miniprot_index" name="Miniprot index" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>build a genome index for miniprot</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        miniprot -d '$output_index' '$input_genome'
    ]]></command>
    <inputs>
        <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds in FASTA format" />
    </inputs>
    <outputs>
        <!-- refine this when miniprot index format is in Galaxy datatypes -->
        <data name="output_index" format="binary" label="Miniprot index on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_genome" value="input_genome.fasta.gz" ftype="fasta" />
            <output name="output_index" ftype="binary">
                <assert_contents>
                    <has_size value="69720149" delta="1000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Pre-index genomic sequences (contigs, scaffolds or chromosomes) for use in the miniprot_ protein to genome alignment tool.

        .. _miniprot: https://github.com/lh3/miniprot
    ]]></help>
    <expand macro="citation"></expand>
</tool>