Mercurial > repos > dfornika > artic_margin_cons_medaka
comparison artic_margin_cons_medaka.xml @ 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 |
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| 6:f52f0a2778f8 | 7:be08b76fd78b |
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| 4 <requirement type="package" version="0.6.8">pyvcf</requirement> | 4 <requirement type="package" version="0.6.8">pyvcf</requirement> |
| 5 <requirement type="package" version="1.76">biopython</requirement> | 5 <requirement type="package" version="1.76">biopython</requirement> |
| 6 <requirement type="package" version="1.9">samtools</requirement> | 6 <requirement type="package" version="1.9">samtools</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 ln -s '${input_alignment}' '${input_alignment.element_identifier}' && | 9 ln -s '${input_alignment}' '${input_alignment.element_identifier}.bam' && |
| 10 samtools index '${input_alignment.element_identifier}' && | 10 samtools index '${input_alignment.element_identifier}.bam' && |
| 11 ln -s '${input_variants}' '${input_variants.element_identifier}.vcf' && | |
| 11 python '${__tool_directory__}/margin_cons_medaka.py' | 12 python '${__tool_directory__}/margin_cons_medaka.py' |
| 12 --depth '${minimum_depth}' | 13 --depth '${minimum_depth}' |
| 13 --quality '${minimum_quality}' | 14 --quality '${minimum_quality}' |
| 14 '${ref_fasta}' | 15 '${ref_fasta}' |
| 15 '${input_variants}' | 16 '${input_variants.element_identifier}.vcf' |
| 16 '${input_alignment.element_identifier}' | 17 '${input_alignment.element_identifier}.bam' |
| 17 > '${consensus_fasta}' | 18 > '${consensus_fasta}' |
| 18 2> '${report}' | 19 2> '${report}' |
| 19 ]]></command> | 20 ]]></command> |
| 20 <inputs> | 21 <inputs> |
| 21 <param name="ref_fasta" type="data" format="fasta" label="Reference Sequence"/> | 22 <param name="ref_fasta" type="data" format="fasta" label="Reference Sequence"/> |