<!-- The tool is broken with current version of HUMAnN. Once it will be fixed, we can update this wrapper and add the XML extension to enable it -->
<tool id="humann_infer_taxonomy" name="Infex taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>for "unclassified" taxonomy in HUMAnN generated gene families</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_infer_taxonomy
    --input '$input'
    --output '$output'
    --level '$level'
    --database '$database.fields.path'
    --mode '$mode'
    --lca-choice '$lca_choice'
    --threshold $threshold
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Gene family table"/>
        <param argument="--level" type="select" label="Desired level for taxonomic estimation/summation">
            <option value="Kingdom">Kingdom</option>
            <option value="Phylum">Phylum</option>
            <option value="Class">Class</option>
            <option value="Order">Order</option>
            <option value="Family" selected="true">Family</option>
            <option value="Genus">Genus</option>
        </param>
        <param argument="--database" type="select" label="UniRef-specific taxonomy database">
            <options from_data_table="humann_utility_mapping">
                <validator message="No utility mapping is available" type="no_options" />
                <filter type="regexp" column="2" value="tol-lca" />
            </options>
        </param>
        <param argument="--mode" type="select" label="Rows to include in the estimation/summation">
            <option value="c_tmode" selected="true">Totals</option>
            <option value="c_umode">Unclassified</option>
            <option value="c_smode">Stratified</option>
        </param>
        <param argument="--lca-choice" type="select" label="Per-gene taxonomic annotation to consider">
            <option value="source_tax">Source taxonomy</option>
            <option value="uniref_lca">UniRef lowest common ancestor (LCA)</option>
            <option value="humann_lca" selected="true">HUMAnN lowest common ancestor (LCA)</option>
        </param>
        <param argument="--threshold" type="float" value="1e-3" label="Minimum frequency for a new taxon to be included"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value=""/>
            <param name="level" value="Kingdom"/>
            <param name="database" value=""/>
            <param name="mode" value="c_tmode"/>
            <param name="lca_choice" value="source_tax"/>
            <param name="threshold" value="1e-3"/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text=""/>
                    <has_line line=""/>
                    <has_line_matching expression=""/>
                    <has_n_columns n=""/>
                    <has_size value="" delta=""/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Based on the lowest common ancestor (LCA) annotation
of each UniRef50/90 cluster, this tool infers approximate taxonomy 
for unclassified features at a target level of resolution.

It will modify features of known genus/species to match 
target level.
    ]]></help>
    <expand macro="citations"/>
</tool>
