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comparison guppy_basecaller.xml @ 7:6977341bd461 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy commit 7c2a0f6b17d2d4de6505a374f1b2fe49c6568c8d
author artbio
date Sat, 13 Jul 2024 11:56:59 +0000
parents 78d793671a9e
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6:78d793671a9e 7:6977341bd461
1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.2" python_template_version="3.8"> 1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="6.5.7+galaxy0" profile="23.0">
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 6
7 #for $file in $infiles: 7 #for $file in $infiles:
8 ln -s $file ${file.element_identifier}.fast5 && 8 ln -s $file ${file.element_identifier}.fast5 &&
9 #end for 9 #end for
10 tar xf $config && 10 tar xf $config &&
11 guppy_basecaller -i . 11 guppy_basecaller -i .
12 --save_path out 12 --save_path "out"
13 --data_path . 13 --data_path "."
14 --config *.cfg 14 --config *.cfg
15 --num_callers 4 15 --num_callers \${GALAXY_SLOTS:-2}
16 --records_per_fastq 0 16 --records_per_fastq 0
17 --cpu_threads_per_caller \${GALAXY_SLOTS:-2} 17 --cpu_threads_per_caller 1
18 --disable_pings 18 --disable_pings
19 ### --qscore_filtering 19 && cat out/pass/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq
20 ### --calib_detect 20 && echo "guppy must be installed system-wide from ONT linux packages" > $discloser
21 && cat out/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq
22 ]]></command> 21 ]]></command>
23 <inputs> 22 <inputs>
24 <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/> 23 <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
25 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/> 24 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
26 </inputs> 25 </inputs>
27 <outputs> 26 <outputs>
28 <data name="output_fastq" format="fastqsanger" /> 27 <data name="output_fastq" format="fastqsanger" label="Guppy base calling" />
28 <data name="discloser" format="txt" label="Guppy Discloser" />
29 </outputs> 29 </outputs>
30 <help><![CDATA[ 30 <help><![CDATA[
31 A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files, 31 A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,
32 and a configuration in the form of a tar file. 32 and a configuration in the form of a tar file.
33 33