<tool id="mycrobiota-make-multi-otutable" name="Make multisample OTUtable" version="0.1">
    <description>from a shared and taxonomy file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/mycrobiota.py'
            --command make_multi_otutable
            --shared_file '$shared_file'
            --taxonomy '$taxonomy'
            --level $level
    ]]></command>
    <inputs>
        <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
        <param argument="--shared_file" type="data" optional="true" format="mothur.shared" label="Supply a mothur shared file" help=""/>
        <param argument="--level" type="select" optional="true" label="label - pick (one) OTU Label" help="leave blank for collections, will try to determine level from element names">
            <options>
                <filter type="data_meta" ref="shared_file" key="labels"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="multi_otutable" format="tabular" from_work_dir="multi_otutable.tsv" label="Multisample otutable on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="taxonomy" value="multisample.taxonomy"/>
            <param name="shared_file" ftype="mothur.shared" value="example.mothur.shared"/>
            <param name="level" value="0.03"/>
            <output name="multi_otutable" file="shared_with_taxonomy.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
        help text goes here
    ]]></help>
    <expand macro="citations"/>
</tool>