Mercurial > repos > artbio > guppy_basecaller
changeset 3:1ca87a2e5edc draft default tip
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit 7e989732e55eb13a0198a6631e2952c154725a5e"
| author | artbio |
|---|---|
| date | Tue, 04 May 2021 16:39:59 +0000 |
| parents | 43246680b014 |
| children | |
| files | guppy_basecaller.xml |
| diffstat | 1 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/guppy_basecaller.xml Thu Nov 19 00:02:35 2020 +0000 +++ b/guppy_basecaller.xml Tue May 04 16:39:59 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.4" python_template_version="3.5"> +<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.1" python_template_version="3.5"> <description>A simple wrapper for guppy basecaller that depends on configuration files</description> <requirements> </requirements> @@ -16,17 +16,16 @@ --records_per_fastq 0 --cpu_threads_per_caller \${GALAXY_SLOTS:-2} --disable_pings - --qscore_filtering +### --qscore_filtering ### --calib_detect + && cat out/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq ]]></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="guppy_result" format="fastq"> - <discover_datasets directory="out/PASS" ext="fastq" pattern=".+\.fastq" visible="true"/> - </data> + <data name="output_fastq" format="fastqsanger" /> </outputs> <help><![CDATA[ A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,