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comparison artic_minion.xml @ 7:f5643712dca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
author iuc
date Mon, 31 Jan 2022 10:12:30 +0000
parents f212134e204c
children 6f52ebc01098
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6:f212134e204c 7:f5643712dca7
32 --scheme-directory 'scheme' 32 --scheme-directory 'scheme'
33 --medaka 33 --medaka
34 --medaka-model '$medaka_model' 34 --medaka-model '$medaka_model'
35 $bwa 35 $bwa
36 'name/V1' 36 'name/V1'
37 '${read_file.element_identifier}' 37 ## enclose the sample name in extra single quotes because
38 ## the minion pipeline script doesn't care about passing
39 ## its arguments safely.
40 "'"'${read_file.element_identifier}'"'"
38 && bgzip -f '${read_file.element_identifier}.fail.vcf' 41 && bgzip -f '${read_file.element_identifier}.fail.vcf'
42 ## remove enclosing single-quotes from header of output consensus fasta
43 && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" ${read_file.element_identifier}.consensus.fasta
39 ]]></command> 44 ]]></command>
40 <inputs> 45 <inputs>
41 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> 46 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
42 <param argument="--normalise" type="integer" min="0" value="0" 47 <param argument="--normalise" type="integer" min="0" value="0"
43 label="Coverage normalisation depth" 48 label="Coverage normalisation depth"