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annotate guppy_basecaller.xml @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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children 6af9afd405e9
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1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.0" python_template_version="3.5">
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2 <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
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3 <requirements>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 ln -s $infile input.fast5 &&
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7 tar xf $config &&
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8 guppy_basecaller -i . -s out -d . -c *.cfg
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9 ]]></command>
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10 <inputs>
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11 <param name="infile" type="data" format="h5" label="Fast5 input"/>
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12 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
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13 </inputs>
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14 <outputs>
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15 <data name="results" format="fastq">
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16 <discover_datasets directory="out" ext="fastq" pattern=".+\.fastq" visible="true"/>
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17 </data>
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18 </outputs>
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19 <help><![CDATA[
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20 A wrapper for guppy basecaller. This expects two inputs: a fast5 file, and a configuration in the form of a tar file.
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21
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22 You can find configurations at https://github.com/nanoporetech/rerio, and in particular the directory https://github.com/nanoporetech/rerio/basecall_models.
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23
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24 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'
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25
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26 When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?).
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27
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28 The result should be a fastq file.
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29 ]]></help>
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30 </tool>