Mercurial > repos > artbio > guppy_basecaller

comparison guppy_basecaller.xml @ 5:dd0cccf3a62f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit 067a2f51c9f4c92c72079d27321e502ca428945f"
author artbio
date Sat, 28 Nov 2020 16:21:21 +0000
parents bc53d2ba84c4
children 78d793671a9e
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4:bc53d2ba84c4 5:dd0cccf3a62f
1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.0" python_template_version="3.5"> 1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.1" 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
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 && cat out/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <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"/>
25 <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"/>
26 </inputs> 26 </inputs>