<tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5">
    <description>compare a list of genomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
         @PREPARE_GENOMES@         
         dRep compare outdir
         @GENOME_COMPARISON_OPTIONS@
         @CLUSTERING_OPTIONS@
         @TAXONOMY_OPTIONS@
         @WARNING_OPTIONS@        
         @GENOMES@
    ]]></command>
    <inputs>
        <expand macro="genomes"/>
        <expand macro="genome_comparison_options"/>
        <expand macro="clustering_options"/>
        <expand macro="taxonomy_options"/>
        <expand macro="warning_options"/>
        <expand macro="select_outputs"/>
    </inputs>
    <outputs>
        <expand macro="common_outputs" />
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.

usage: drep compare [-p PROCESSORS] [-d] [-h] [-ms MASH_SKETCH]
                    [--S_algorithm {ANIn,goANI,ANImf,gANI}]
                    [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI]
                    [--SkipMash] [--SkipSecondary] [-nc COV_THRESH]
                    [-cm {total,larger}] [--clusterAlg CLUSTERALG] [--run_tax]
                    [--tax_method {percent,max}] [-per PERCENT]
                    [--cent_index CENT_INDEX] [--warn_dist WARN_DIST]
                    [--warn_sim WARN_SIM] [--warn_aln WARN_ALN]
                    [-g [GENOMES [GENOMES ...]]]
                    work_directory


    @GENOMES_HELP@
    @GENOME_COMPARISON_HELP@
    @CLUSTERING_HELP@
    @TAXONOMY_HELP@
    @WARNINGS_HELP@

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