Mercurial > repos > shellac > guppy_basecaller
comparison guppy_basecaller.xml @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 758bc20232e8 |
children | 9b1c78e6ba9c |
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3:758bc20232e8 | 4:79f47841a781 |
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1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.1"> | 1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.2"> |
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. |