Mercurial > repos > iuc > artic_minion
changeset 7:f5643712dca7 draft
"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 |
| files | artic_minion.xml macros.xml |
| diffstat | 2 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- a/artic_minion.xml Wed Oct 06 12:04:58 2021 +0000 +++ b/artic_minion.xml Mon Jan 31 10:12:30 2022 +0000 @@ -34,8 +34,13 @@ --medaka-model '$medaka_model' $bwa 'name/V1' - '${read_file.element_identifier}' + ## enclose the sample name in extra single quotes because + ## the minion pipeline script doesn't care about passing + ## its arguments safely. + "'"'${read_file.element_identifier}'"'" && bgzip -f '${read_file.element_identifier}.fail.vcf' + ## remove enclosing single-quotes from header of output consensus fasta + && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" ${read_file.element_identifier}.consensus.fasta ]]></command> <inputs> <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
--- a/macros.xml Wed Oct 06 12:04:58 2021 +0000 +++ b/macros.xml Mon Jan 31 10:12:30 2022 +0000 @@ -1,5 +1,6 @@ <macros> <token name="@PACKAGE_VERSION@">1.2.1</token> + <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> <xml name="citations"> <citations> <citation type="bibtex">