Mercurial > repos > dfornika > artic_margin_cons_medaka
changeset 2:24c5caa214e7 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"
author | dfornika |
---|---|
date | Wed, 11 Mar 2020 02:14:45 +0000 |
parents | 9fcffca8f6ad |
children | eeb3cb264cb0 |
files | artic_margin_cons_medaka.xml |
diffstat | 1 files changed, 5 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/artic_margin_cons_medaka.xml Wed Mar 11 02:00:01 2020 +0000 +++ b/artic_margin_cons_medaka.xml Wed Mar 11 02:14:45 2020 +0000 @@ -3,14 +3,17 @@ <requirements> <requirement type="package" version="0.6.8">pyvcf</requirement> <requirement type="package" version="1.76">biopython</requirement> + <requirement type="package" version="1.9">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + ln -s '${input_alignment}' alignment.bam && + samtools index alignment.bam && python '${__tool_directory__}/margin_cons_medaka.py' --depth '${minimum_depth}' --quality '${minimum_quality}' '${ref_fasta}' '${input_variants}' - '${input_alignment}' + alignment.bam > '${consensus_fasta}' 2> '${report}' ]]></command> @@ -23,7 +26,7 @@ </inputs> <outputs> <data name="consensus_fasta" format="fasta" label="${tool.name} on ${on_string}: Consensus (.fasta)" /> - <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" /> + <data name="report" format="txt" label="${tool.name} on ${on_string}: Report" /> </outputs> <tests> </tests>