<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.1">
    <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s $infile input.fast5 &&
        tar xf $config &&
        guppy_basecaller -i . -s out -d . -c *.cfg
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="h5" label="Fast5 input"/>
        <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
    </inputs>
    <outputs>
        <data name="results" format="fastq">
            <discover_datasets directory="out" ext="fastq" pattern=".+\.fastq" visible="true"/>
        </data>
          <!--<data format="fastq" name="output" label="Modified FASTQ"/>-->
    </outputs>
    <help><![CDATA[
        A wrapper for guppy basecaller. This expects two inputs: a fast5 file, and a configuration in the form of a tar file. 

        You can find configurations at https://github.com/nanoporetech/rerio, and in particular the directory https://github.com/nanoporetech/rerio/basecall_models. 

        Each file there contains a URL you can download to use, for example https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_rna2_r941_min_flipflop_v001 points to 'https://nanoporetech.box.com/shared/static/84e1jeudx8lr8ay7e9u1ebnvx3bk2kjf.tgz'

        When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?).

        The result should be a fastq file.
    ]]></help>
</tool>