<tool id="cat_summarise" name="CAT summarise" version="@VERSION@.0">
    <description>annotate with taxonomic classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    CAT summarise -c '$contigs_fasta' -i '$input'
    -o output_names_summary.txt
    && @TXT2TSV@ -i output_names_summary.txt -o $output
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="classification.official_names.txt"
            help="The classication must be made with only_official names"/>
        <param name="contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta" 
            help="Required if a contig2classification.names"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
            <param name="contigs_fasta" ftype="fasta" value="configs.fasta"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Firmicutes" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**CAT summarise** 
Produce a summary report of assignments to the ofifcial taxonomic names. 

@COMMON_HELP@
    ]]></help>
    <expand macro="citations" />
</tool>