view dorado_pod5_convert.xml @ 0:18a8d140ec6f draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f

<tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
    <description>converter for raw Oxford Nanopore data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command><![CDATA[

mkdir input_fast5

&&

tar -xf '$fast5_in' -C input_fast5

&&

pod5 convert fast5
--threads \${GALAXY_SLOTS:-4}
--recursive
--output output.pod5
input_fast5

    ]]>
    </command>
    <inputs>
        <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive."/>
    </inputs>
    <outputs>
        <!-- FIXME: add pod5 datatype to Galaxy and change here.
        https://github.com/galaxyproject/galaxy/pull/18419 -->
        <data format="binary" name="pod5_out" label="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/>
            <output name="pod5_out" ftype="binary">
                <assert_contents>
                    <has_size value="519736" delta="50000"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/>
            <output name="pod5_out" ftype="binary">
                <assert_contents>
                    <has_size value="950136" delta="90000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Convert fast5 to `pod5 <https://github.com/nanoporetech/pod5-file-format>`__ for basecalling with Dorado.

        Combine all your fast5 files into a single tar archive, and optionally
        compress the archive with Gzip, Bzip2 or XZ, before uploading it to
        Galaxy.

            ]]></help>
</tool>