<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 argument="--input" type="data" format="tabular" label="classification.official_names.txt"
            help="The classication must be made with only_official names"/>
        <param argument="--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="contigs.fasta"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Firmicutes" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**CAT summarise** 

Summarise taxonomic asignemts from anamed CAT or BAT classification file. 

Required arguments:
  -i, --input_file     Path to named CAT contig classification file or BAT
                       bin classification file. Currently only official ranks
                       are supported, and only classification files
                       containing a single classification per contig / bin.

Optional arguments:
  -c, --contigs_fasta
                        Path to contigs fasta file. This is required if you
                        want to summarise a contig classification file.

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