gatk_bqsr.xml

<tool id="gatk_bqsr" name="GATK BQSR" version="1.0.0">
    <description>base quality score recalibration</description>
    <requirements>
        <container type="docker">gatk</container>
    </requirements>
    <command interpreter="bash">$runscript</command>
    <inputs>
        <param format="bam"   type="data" name="input_bam"      label="Input BAM" help="" />
        <param format="vcf"   type="data" name="known_sites"    label="Known SNP sites VCF" />
        <param format="fasta" type="data" name="reference"      label="Reference Genome" />
        <param type="boolean" name="emit_oq" label="Emit Original Quality Scores" truevalue="--emit_original_quals" falsevalue="" checked="yes"/>
    </inputs>

    <outputs>
        <data format="txt" name="output_report" label="BQSR Report" from_work_dir="recal_data.table"/>
        <data format="bam" name="output_bam" label="BQSR BAM" from_work_dir="output.bam"/>
    </outputs>

    <configfiles>
        <configfile name="runscript">#!/bin/bash
set -e
ln -s ${input_bam} input.bam
ln -s ${input_bam.metadata.bam_index} input.bam.bai
ln -s ${reference} reference.fasta
ln -s ${known_sites} known_sites.vcf

samtools faidx reference.fasta
java -jar /opt/picard/CreateSequenceDictionary.jar R=reference.fasta O=reference.dict

java -jar /opt/GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-R reference.fasta \
-I input.bam \
-knownSites known_sites.vcf \
-nct \${GALAXY_SLOTS:-4} \
-o recal_data.table

java -jar /opt/GenomeAnalysisTK.jar \
-T PrintReads \
-R reference.fasta \
${emit_oq} \
-I input.bam \
-nct \${GALAXY_SLOTS:-4} \
-BQSR recal_data.table \
-o output.bam

        </configfile>
    </configfiles>

    <stdio>
        <exit_code range="1:" level="fatal" />
        <regex match="ERROR"
            source="both"
            level="fatal"
            description="Error running BQSR" />
    </stdio>
    <help>

    </help>

    <tests>
        <test>
        </test>
    </tests>

</tool>