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