Mercurial > repos > artbio > guppy_basecaller
changeset 7:6977341bd461 draft default tip
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 |
| children | |
| files | guppy_basecaller.xml |
| diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/guppy_basecaller.xml Sun Dec 10 15:06:44 2023 +0000 +++ b/guppy_basecaller.xml Sat Jul 13 11:56:59 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.2" python_template_version="3.8"> +<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="6.5.7+galaxy0" profile="23.0"> <description>A simple wrapper for guppy basecaller that depends on configuration files</description> <requirements> </requirements> @@ -9,23 +9,23 @@ #end for tar xf $config && guppy_basecaller -i . - --save_path out - --data_path . + --save_path "out" + --data_path "." --config *.cfg - --num_callers 4 + --num_callers \${GALAXY_SLOTS:-2} --records_per_fastq 0 - --cpu_threads_per_caller \${GALAXY_SLOTS:-2} + --cpu_threads_per_caller 1 --disable_pings -### --qscore_filtering -### --calib_detect - && cat out/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq + && cat out/pass/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq + && echo "guppy must be installed system-wide from ONT linux packages" > $discloser ]]></command> <inputs> <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/> <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/> </inputs> <outputs> - <data name="output_fastq" format="fastqsanger" /> + <data name="output_fastq" format="fastqsanger" label="Guppy base calling" /> + <data name="discloser" format="txt" label="Guppy Discloser" /> </outputs> <help><![CDATA[ A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,