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comparison 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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2:6af9afd405e9 3:758bc20232e8
1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.0" python_template_version="3.5"> 1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.1">
2 <description>A simple wrapper for guppy basecaller that depends on configuration files</description> 2 <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 ln -s $infile input.fast5 && 6 ln -s $infile input.fast5 &&
10 <inputs> 10 <inputs>
11 <param name="infile" type="data" format="h5" label="Fast5 input"/> 11 <param name="infile" type="data" format="h5" label="Fast5 input"/>
12 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/> 12 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
13 </inputs> 13 </inputs>
14 <outputs> 14 <outputs>
15 <!--<data name="results" format="fastq"> 15 <data name="results" format="fastq">
16 <discover_datasets directory="out" ext="fastq" pattern=".+\.fastq" visible="true"/> 16 <discover_datasets directory="out" ext="fastq" pattern=".+\.fastq" visible="true"/>
17 </data>--> 17 </data>
18 <data format="fastq" name="output" label="Modified FASTQ"/> 18 <!--<data format="fastq" name="output" label="Modified FASTQ"/>-->
19 </outputs> 19 </outputs>
20 <help><![CDATA[ 20 <help><![CDATA[
21 A wrapper for guppy basecaller. This expects two inputs: a fast5 file, and a configuration in the form of a tar file. 21 A wrapper for guppy basecaller. This expects two inputs: a fast5 file, and a configuration in the form of a tar file.
22 22
23 You can find configurations at https://github.com/nanoporetech/rerio, and in particular the directory https://github.com/nanoporetech/rerio/basecall_models. 23 You can find configurations at https://github.com/nanoporetech/rerio, and in particular the directory https://github.com/nanoporetech/rerio/basecall_models.