Mercurial > repos > dfornika > artic_margin_cons_medaka
view artic_margin_cons_medaka.xml @ 4:eb4af87a77ff 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 |
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date | Wed, 11 Mar 2020 02:31:04 +0000 |
parents | 24c5caa214e7 |
children | 47eb99e41bfb |
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<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0+galaxy0"> <description>Generate consensus fasta file from a reference fasta, bam alignment and VCF file</description> <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}' alignment.bam > '${consensus_fasta}' 2> '${report}' ]]></command> <inputs> <param name="ref_fasta" type="data" format="fasta" label="Reference Sequence"/> <param name="input_alignment" type="data" format="bam" label="Input Alignment"/> <param name="input_variants" type="data" format="vcf" label="Input Variants"/> <param name="minimum_depth" type="integer" value="5" min="1" max="500" label="Minimum depth to call a variant"/> <param name="minimum_quality" type="integer" value="0" min="0" max="100" label="Minimum quality to call a variant"/> </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" /> </outputs> <tests> </tests> <help><![CDATA[ ]]></help> <citations> </citations> </tool>