<tool id="red" name="Red" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>repeat masking</description>
    <macros>
        <token name="@TOOL_VERSION@">2018.09.10</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">red</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
mkdir input output &&

ln -s '${input}' input/genome.fa &&

Red
-gnm input/
-msk output/
-rpt output/
-frm 2
-cor \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <param label="Genome sequence to mask" name="input" type="data" format="fasta" />
    </inputs>
    <outputs>
        <data format="fasta" name="masked" from_work_dir="output/genome.msk" />
        <data format="bed" name="bed" from_work_dir="output/genome.bed" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="small.fa" />
            <output name="masked" file="small.msk" />
            <output name="bed" file="small.bed" />
        </test>
    </tests>
    <help><![CDATA[
This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD.

An intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
    ]]></help>
    <citations>
        <citation type="doi">10.1186/s12859-015-0654-5</citation>
    </citations>
</tool>