<tool id="scrappie_raw" name="Scrappie (raw)" version="1.0.0">

    <description>ONT development basecaller</description>

    <!-- ***************************************************************** -->
   
    <!--
    <requirements>
        <requirement type="package" version="1.0.0">scrappie</requirement>
    </requirements>
    -->

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    <version_command>scrappie version | perl -wnE'print "$1\n" for /scrappie (.+)/g'</version_command>

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    <command detect_errors="aggressive">
    <![CDATA[

    python3 $__tool_directory__/scrappie_raw.py $input $output \${GALAXY_SLOTS:-1}

    ]]>
    </command>

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    <inputs>

        <param name="input" type="data" format="fast5_archive" label="Input reads" />

    </inputs>

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    <outputs>

        <data name="output" format="fasta" label="${tool.name} on ${on_string} (called.fasta)" />

    </outputs>

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    <tests>
        <!-- multithreaded output is non-deterministic, so simply compare file
        sizes -->
        <test>
            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
            <output name="output" file="test_data.fasta" compare="sim_size" delta="0" />
        </test>
    </tests>

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    <help>
    <![CDATA[

**Description**

Scrappie provides recurrent neural network basecalling for Oxford Nanopore
MinION data. It is a technology demonstrator for the Oxford Nanopore
Research Algorithms group. It is designed for improved calling of
homopolymers over nanonet. Scrappie is provided unsupported by Oxford
Nanopore Technologies.

The Galaxy wrapper has modified scrappie to take a gzip tarball of FAST5 reads
as input, such as can be produced by `poretools combine`, and always outputs a
single FASTA file.

This is the raw basecaller.

    ]]>
    </help>

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    <citations>
    </citations>

</tool>