<tool id="checkm_analyze" name="CheckM analyze" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Identify marker genes in bins and calculate genome statistics
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
@BIN_INPUTS@

checkm analyze
    '$marker_file'
    'bins'
    'output'
    $ali
    $nt
    $genes
    --extension 'fasta'
    --threads \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <expand macro="bin_inputs" />
        <expand macro="marker_file" />
        <expand macro="analyze_params"/>
        <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
            <expand macro="analyze_extra_output_options" />
        </param>
    </inputs>
    <outputs>
        <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
        </collection>
        <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats" />
        <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" />
        <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
            <filter>ali and 'hmmer_analyze_ali' in extra_outputs</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <conditional name="bins">
                <param name="select" value="collection"/>
                <param name="bins_coll">
                    <collection type="list">
                        <element name="637000110" ftype="fasta" value="637000110.fna"/>
                    </collection>
                </param>
            </conditional>
            <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
            <param name="ali" value="false"/>
            <param name="nt" value="false"/>
            <param name="genes" value="false"/>
            <param name="extra_outputs" value=""/>
            <output_collection name="hmmer_analyze" count="1">
                <element name="637000110" ftype="txt">
                    <assert_contents>
                        <has_text text="target name"/>
                        <has_text text="AC_000091_859"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="bin_stats_analyze" ftype="tabular">
                <assert_contents>
                    <has_text text="637000110"/>
                    <has_text text="GC"/>
                    <has_text text="GC std"/>
                </assert_contents>
            </output>
            <output name="checkm_hmm_info" ftype="zip">
                <assert_contents>
                    <has_size value="99600" delta="500"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <conditional name="bins">
                <param name="select" value="collection"/>
                <param name="bins_coll">
                    <collection type="list">
                        <element name="637000110" ftype="fasta" value="637000110.fna"/>
                    </collection>
                </param>
            </conditional>
            <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
            <param name="ali" value="true"/>
            <param name="nt" value="true"/>
            <param name="genes" value="false"/>
            <param name="extra_outputs" value="hmmer_analyze_ali"/>
            <output_collection name="hmmer_analyze" count="1">
                <element name="637000110" ftype="txt">
                    <assert_contents>
                        <has_text text="target name"/>
                        <has_text text="AC_000091_859"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="bin_stats_analyze" ftype="tabular">
                <assert_contents>
                    <has_text text="637000110"/>
                    <has_text text="GC"/>
                    <has_text text="GC std"/>
                </assert_contents>
            </output>
            <output name="checkm_hmm_info" ftype="zip">
                <assert_contents>
                    <has_size value="99600" delta="500"/>
                </assert_contents>
            </output>
            <output_collection name="hmmer_analyze_ali" count="1">
                <element name="637000110" ftype="txt">
                    <assert_contents>
                        <has_text text="hmmsearch"/>
                        <has_text text="Query"/>
                        <has_text text="ACCA"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This command identifies marker genes in bins and calculates genome statistics
    ]]></help>
    <expand macro="citations"/>
</tool>