<tool id="checkm_lineage_set" name="CheckM lineage_set" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Infer lineage-specific marker sets for each bin
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
@HMM_MARKER_STATS_INPUTS@
mkdir 'inputs/storage/tree' &&
ln -s '$concatenated_tre' 'inputs/storage/tree/concatenated.tre' &&

checkm lineage_set
    'inputs'
    '$marker'
    --unique $unique
    --multi $multi
    $force_domain
    $no_refinement
    ]]></command>
    <inputs>
        <expand macro="hmm_marker_stats_inputs"/>
        <param name="concatenated_tre" type="data" format="phyloxml" label="Concatenated tree" help="Output of the CheckM tree tool"/>
        <expand macro="lineage_set_params" />
    </inputs>
    <outputs>
        <expand macro="marker_output" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
            <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
            <param name="hmmer_tree">
                <collection type="list">
                    <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
                </collection>
            </param>
            <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
            <param name="unique" value="10"/>
            <param name="multi" value="10"/>
            <param name="force_domain" value="false"/>
            <param name="no_refinement" value="false"/>
            <output name="marker" ftype="tabular">
                <assert_contents>
                    <has_text text="637000110"/>
                    <has_text text="Lineage Marker File"/>
                    <has_text text="PF00203"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This command places bins in the genome tree.
    ]]></help>
    <expand macro="citations"/>
</tool>