<tool id="minia" name="Minia" version="@TOOL_VERSION@">
    <description>Short-read assembler based on a de Bruijn graph</description>
    <macros>
        <token name="@TOOL_VERSION@">3.2.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">minia</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set input = 'infile.' + $in.ext
ln -s '$in' '$input' &&

minia
-in '$input'
-kmer-size $kmer_size
#if str($abundance_min):
    -abundance-min $abundance_min
#end if
#if str($abundance_max):
    -abundance-min $abundance_max
#end if
-nb-cores \${GALAXY_SLOTS:-1}
-out output
    ]]></command>
    <inputs>
        <param argument="-in" type="data" format="fasta,fastqsanger,fastqsanger.gz,fasta.gz" label="Reads in FASTA or FASTQ format" />
        <param argument="-kmer-size" type="integer" value="31" min="1" label="Size of a kmer" />
        <param argument="-abundance-min" type="integer" value="" optional="true" min="0" label="Min abundance threshold for solid kmers (default: 2)" />
        <param argument="-abundance-max" type="integer" value="" optional="true" label="Max abundance threshold for solid kmers" />
    </inputs>
    <outputs>
        <data name="output" format="fasta" label="${tool.name} on ${on_string}" from_work_dir="output.contigs.fa" />
    </outputs>
    <tests>
        <test>
            <param name="in" value="ec.fa" />
            <param name="kmer_size" value="21" />
            <param name="abundance_min" value="1" />
            <output name="output" ftype="fasta">
                <assert_contents>
                    <has_text text="LN:i:460 KC:i:2200 km:f:5.000"/>
                    <has_text text="LN:i:637 KC:i:3085 km:f:5.000"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
The output of Minia is a set of contigs.
    ]]></help>
    <citations>
        <citation type="doi">10.1186/1748-7188-8-22</citation>
    </citations>
</tool>