Mercurial > repos > dfornika > artic_margin_cons_medaka
view 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 |
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date | Tue, 17 Mar 2020 22:05:59 +0000 |
parents | f52f0a2778f8 |
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<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0-1005a47+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 '${input_alignment}' '${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.element_identifier}.vcf' '${input_alignment.element_identifier}.bam' > '${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>