<tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@" profile="19.01">
    <description> creates a consensus sequence from nanopore sequencing data</description>
    <macros>
        <token name="@VERSION@">0.11.5</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">medaka</requirement>
    </requirements>
    <version_command>medaka --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        medaka_consensus 
        -i '${basecalled}' 
        -d '${draft}' 
        -o out_dir 
        -t \${GALAXY_SLOTS:-4} 
        -m '${model}' > log.txt
    ]]>    </command>

    <inputs>
        <param name="basecalled" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz"
            label="Basecalled data"/>
        <param name="draft" type="data" format="fasta,fasta.gz" label="Draft assemblies"
            help="The input assembly should be preprocessed with racon"/>
        <param name="model" type="select" label="Model">
            <option value="r941_min_fast_g303">r941_min_fast_g303</option>
            <option value="r941_min_high_g303" selected="True">r941_min_high_g303</option>
            <option value="r941_min_high_g330">r941_min_high_g330</option>
            <option value="r941_min_high_g344">r941_min_high_g344</option>
            <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
            <option value="r941_prom_high_g303">r941_prom_high_g303</option>
            <option value="r941_prom_high_g344">r941_prom_high_g344</option>
            <option value="r941_prom_high_g330">r941_prom_high_g330</option>
            <option value="r10_min_high_g303">r10_min_high_g303</option>
            <option value="r10_min_high_g340">r10_min_high_g340</option>
            <option value="r103_min_high_g345">r103_min_high_g345</option>
            <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
            <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
            <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
        </param>
    </inputs>
    <outputs>
        <!-- <collection name="list_output" type="list" label="Output">
        <discover_datasets pattern="__name_and_ext__" directory="out_dir"/>
    </collection> -->
        <data name="consensus" format="fasta" label="${tool.name} on ${on_string}: consensus" from_work_dir="out_dir/consensus.fasta"/>
        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/>
    </outputs>
    <tests>
        <test>
            <param name="draft" value="plasmid.fasta" />
            <param name="basecalled" value="reads.fastq" />
            <param name="model" value="r941_min_fast_g303"/>
            <output name="consensus" file="medaka/consensus.fasta" ftype="fasta" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

medaka is a tool to create a consensus sequence from nanopore sequencing data.
This task is performed using neural networks applied from a pileup of individual sequencing
reads against a draft assembly. It outperforms graph-based methods operating on basecalled data,
and can be competitive with state-of-the-art signal-based methods, whilst being much faster.


    ]]></help>
</tool>