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annotate guppy_basecaller.xml @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 6af9afd405e9
children 79f47841a781
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1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.1">
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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 <!--<data format="fastq" name="output" label="Modified FASTQ"/>-->
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19 </outputs>
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20 <help><![CDATA[
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21 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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22
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23 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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25 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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27 When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?).
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29 The result should be a fastq file.
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30 ]]></help>
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31 </tool>