<tool id="cat_contigs" name="CAT contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <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 contigs 
    -c '$contigs_fasta'
    @CAT_DB@
    @USE_INTERMEDIATES@
    @CUSTOM_SETTINGS@
    @DIAMOND_OPTIONS@
    && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt
    @ADD_NAMES@
    @SUMMARISE@
    ]]></command>
    <inputs>
        <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/>
        <expand macro="cat_db" />
        <expand macro="use_intermediates" />
        <expand macro="custom_settings_contigs" />
        <expand macro="diamond_options" />
        <expand macro="add_names" />
        <expand macro="summarise" />
        <expand macro="select_cat_outputs" />
    </inputs>
    <outputs>
        <expand macro="outputs" />
    </outputs>
    <tests>
        <test>
            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="contig2classification"/>
            <output name="contig2classification">
                <assert_contents>
                    <has_text text="contig_38063" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="predicted_proteins_faa"/>
            <conditional name="names">
                <param name="add_names" value="both"/>
            </conditional>
            <param name="summarise" value="classification"/>
            <output name="predicted_proteins_faa">
                <assert_contents>
                    <has_text text=">contig_9952" />
                </assert_contents>
            </output>
            <output name="orf2lca_names">
                <assert_contents>
                    <has_text text="Bacilli" />
                </assert_contents>
            </output>
            <output name="classification_summary">
                <assert_contents>
                    <has_text text="Bacilli" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**CAT contigs**

Classifiy metagenomics contigs.

@COMMON_HELP@

@OUTPUTS_HELP@


**CAT contigs**

Run Contig Annotation Tool (CAT).

Required arguments:
  -c, --contigs_fasta    Path to contigs fasta file.
  -d, --database_folder  Path to folder that contains database files.
  -t, --taxonomy_folder  Path to folder that contains taxonomy files.


@OPTIONS_HELP@

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