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comparison artic_minion.xml @ 8:6f52ebc01098 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 42a048391200da4c664650f7e7665c97ace584ee"
author iuc
date Mon, 07 Feb 2022 09:41:30 +0000
parents f5643712dca7
children
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7:f5643712dca7 8:6f52ebc01098
38 ## the minion pipeline script doesn't care about passing 38 ## the minion pipeline script doesn't care about passing
39 ## its arguments safely. 39 ## its arguments safely.
40 "'"'${read_file.element_identifier}'"'" 40 "'"'${read_file.element_identifier}'"'"
41 && 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 42 ## remove enclosing single-quotes from header of output consensus fasta
43 && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" ${read_file.element_identifier}.consensus.fasta 43 && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" '${read_file.element_identifier}.consensus.fasta'
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <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"/>
47 <param argument="--normalise" type="integer" min="0" value="0" 47 <param argument="--normalise" type="integer" min="0" value="0"
48 label="Coverage normalisation depth" 48 label="Coverage normalisation depth"