<tool id="albacore_1D" name="Albacore 1D" version="2.0.2b">

    <description>ONT production basecaller</description>

    <!-- ***************************************************************** -->
   
    <!--
    <requirements>
        <requirement type="package" version="2.0.2">albacore</requirement>
    </requirements>
    -->

    <!-- ***************************************************************** -->

    <version_command>read_fast5_basecaller.py --version | perl -wnE'print "$1\n" for /\(version ([^\)]+)\)/g'</version_command>

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

    python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux $disable_filt \${GALAXY_SLOTS:-1}

    ]]>
    </command>

    <!-- ***************************************************************** -->

    <inputs>

        <param name="input" type="data" format="fast5.tar" label="Input reads" />
        <param name="out_format" type="select" label="Output format">
            <option value="fastq" selected="true">fastq</option>
            <option value="fast5">fast5</option>
        </param>
        <param name="demux" type="boolean" checked="false" label="Demultiplex" />
        <param name="disable_filt" type="boolean" checked="false" label="Disable quality filtering" />
        <param name="output_table" type="boolean" checked="false" label="Include table in output" />

    </inputs>

    <!-- ***************************************************************** -->

    <outputs>

        <data name="output" format="fastq" label="${tool.name} on ${on_string} (reads)">
            <filter>demux is False</filter>
            <change_format>
                <when input="out_format" value="fast5" format="fast5.tar.gz" />
            </change_format>
        </data>
        <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string} (reads)">
            <filter>demux is True and out_format == 'fastq'</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fastqsanger" />
        </collection>
        <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)">
            <filter>demux is True and out_format == 'fast5'</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
        </collection>
        <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)">
            <filter>output_table is True</filter>
        </data>

    </outputs>

    <!-- ***************************************************************** -->

    <tests>
        <test>
            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
            <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
        </test>
        <test>
            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
            <param name="disable_filt" value="true" />
            <output name="output" file="test_data_nofilt.fastq" compare="sim_size" delta="0"/>
        </test>
    </tests>

    <!-- ***************************************************************** -->

    <help>
    <![CDATA[

**Description**

Albacore is a tool for basecalling Oxford Nanopore reads. It is distributed by
ONT to authorized community members only and thus is not packaged through
Galaxy or Bioconda. End users are responsible for installing and testing the
albacore software themselves and ensuring that it is in the galaxy user $PATH.

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

This is the 1D basecaller.

    ]]>
    </help>

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    <citations>
    </citations>

</tool>