add_rank_names_to_phyloseq.xml

<tool id="add_rank_names_to_phyloseq" name="Add Rank Names to Phyloseq Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Add taxonomy rank names to a phyloseq object</description> 
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
Rscript '${__tool_directory__}/add_rank_names_to_phyloseq.R' --input '$input'  --output '$output' --ranks '$ranks'
]]></command>

    <inputs>
        <expand macro="phyloseq_input"/>
        <param name="ranks" type="text" label="Comma-separated list of taxonomy ranks"  value="Kingdom,Phylum,Class,Order,Family,Genus,Species"/>
    </inputs>
    
    <outputs>
        <data name="output" format="phyloseq"/>
    </outputs>

     <tests>
        <test>
            <param name="input" value="output.phyloseq" ftype="phyloseq"/>
            <param name="ranks" value="Kingdom,Phylum,Class,Order,Family,Genus"/>
            <output name="output" ftype="phyloseq">
                <assert_contents>
                    <has_size value="87125" delta="1000"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>
    This tool adds taxonomy rank names to a phyloseq object in the `tax_table` slot.
    </help>
    <expand macro="citations"/>
</tool>