comparison guppy_basecaller.xml @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

4:79f47841a781

<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.2">
    <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 &&

    <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. 

5:9b1c78e6ba9c

<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.3" python_template_version="3.5">
    <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 &&

    <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="guppy_result" format="fastq">
            <discover_datasets directory="out" ext="fastq" pattern=".+\.fastq" visible="true"/>
        </data>
    </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.