<tool id="samtools_faidx" name="Samtools faidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Index a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
    samtools
        faidx
        '$in_fasta'
        --fai-idx '$output'
    ]]></command>
    <inputs>
        <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" />
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="in_fasta" value="samtools_fastx-out1-2.fasta" />
            <output name="output" file="out.tabular" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.

Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command.
    ]]></help>
    <expand macro="citations"/>
</tool>