Mercurial > repos > dfornika > artic_margin_cons_medaka
changeset 7:be08b76fd78b draft default tip
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
author | dfornika |
---|---|
date | Tue, 17 Mar 2020 22:05:59 +0000 |
parents | f52f0a2778f8 |
children | |
files | artic_margin_cons_medaka.xml |
diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/artic_margin_cons_medaka.xml Tue Mar 17 21:42:53 2020 +0000 +++ b/artic_margin_cons_medaka.xml Tue Mar 17 22:05:59 2020 +0000 @@ -6,14 +6,15 @@ <requirement type="package" version="1.9">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - ln -s '${input_alignment}' '${input_alignment.element_identifier}' && - samtools index '${input_alignment.element_identifier}' && + ln -s '${input_alignment}' '${input_alignment.element_identifier}.bam' && + samtools index '${input_alignment.element_identifier}.bam' && + ln -s '${input_variants}' '${input_variants.element_identifier}.vcf' && python '${__tool_directory__}/margin_cons_medaka.py' --depth '${minimum_depth}' --quality '${minimum_quality}' '${ref_fasta}' - '${input_variants}' - '${input_alignment.element_identifier}' + '${input_variants.element_identifier}.vcf' + '${input_alignment.element_identifier}.bam' > '${consensus_fasta}' 2> '${report}' ]]></command>