Mercurial > repos > artbio > guppy_basecaller

comparison guppy_basecaller.xml @ 3:df3f2f852ed5 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit dce10266bcd6c49429740b724d833f109f4e5cad"
author artbio
date Sat, 28 Nov 2020 15:12:30 +0000
parents cfc7ff08ad20
children bc53d2ba84c4
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2:cfc7ff08ad20 3:df3f2f852ed5
1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.5" python_template_version="3.5"> 1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.6" python_template_version="3.5">
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
14 --config *.cfg 14 --config *.cfg
15 --num_callers 4 15 --num_callers 4
16 --records_per_fastq 0 16 --records_per_fastq 0
17 --cpu_threads_per_caller \${GALAXY_SLOTS:-2} 17 --cpu_threads_per_caller \${GALAXY_SLOTS:-2}
18 --disable_pings 18 --disable_pings
19 --qscore_filtering 19 ### --qscore_filtering
20 ### --calib_detect 20 ### --calib_detect
21 && cat *.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output.fastq
21 ]]></command> 22 ]]></command>
22 <inputs> 23 <inputs>
23 <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/> 24 <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
24 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/> 25 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
25 </inputs> 26 </inputs>
26 <outputs> 27 <outputs>
27 <data name="guppy_result" format="fastq"> 28 <data name="output.fastq" format="fastqsanger" />
28 <discover_datasets directory="out/pass" ext="fastq" pattern=".+\.fastq" visible="true"/>
29 </data>
30 </outputs> 29 </outputs>
31 <help><![CDATA[ 30 <help><![CDATA[
32 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,
33 and a configuration in the form of a tar file. 32 and a configuration in the form of a tar file.
34 33