<tool id="humann_strain_profiler" name="Make strain profiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_strain_profiler
    --input '$input'
    --critical_mean $critical_mean
    --critical_count $critical_count
    --pinterval $pinterval_1 $pinterval_2
    --critical_samples $critical_samples
#if str($limit) != ''
    --limit '$limit'
#end if
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular,biom1" label="Merged gene families output for two or more samples"/>
        <param argument="--critical_mean" type="float" value="10.0" label="Default mean non-zero gene abundance for inclusion"/>
        <param argument="--critical_count" type="integer" value="500" label="Default non-zero number of genes for inclusion"/>
        <param name="pinterval_1" type="float" value="1e-10" label="Low prevalence threshold" help="Only genes with prevalence higher than the threshold are allowed"/>
        <param name="pinterval_2" type="float" value="1" label="High prevalence threshold" help="Only genes with prevalence lower than the threshold are allowed"/>
        <param argument="--critical_samples" type="integer" value="2" label="Threshold number of samples having strain"/>
        <param argument="--limit" type="text" value="" optional="true" label="Limit output to species matching a particular pattern?" help="e.g. 'Streptococcus'"/>
    </inputs>
    <outputs>
        <collection name="output" type="list">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)-strain_profile.tsv" format="tabular" directory="."/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="strain_profiler-input.txt"/>
            <param name="critical_mean" value="1"/>
            <param name="critical_count" value="2"/>
            <param name="pinterval_1" value="1e-10"/>
            <param name="pinterval_2" value="1"/>
            <param name="critical_samples" value="2"/>
            <output_collection name="output" type="list">
                <element name="s1" ftype="tabular">
                    <assert_contents>
                        <has_text text="A|g1.s1"/>
                        <has_text text="10.0"/>
                        <has_n_columns n="4"/>
                    </assert_contents>
                </element>
                <element name="s2" ftype="tabular">
                    <assert_contents>
                        <has_text text="A|g1.s2"/>
                        <has_text text="10.0"/>
                        <has_n_columns n="4"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This tool makes strain profiles, based on the principle of detecting variable 
presence and absence of gene families within a species
that is otherwise well-covered in multiple samples.
    ]]></help>
    <expand macro="citations"/>
</tool>