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gatk4.xml
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gatk4.xml
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<tool id="gatk4_docker" name="GATK 4 (Docker)" version="4">
<description>Genome Analysis Toolkit 4 in a Docker container</description>
<requirements>
<container type="docker">broadinstitute/gatk:4.1.3.0</container>
</requirements>
<command>
<![CDATA[
bash '${__tool_directory__}/gatk4-galaxy.sh' '${reference_fasta}' '${input_bam}' '${dbsnp}' '${emit_ref_confidence}' '${max_alternate_alleles}' '${min_base_quality_score}' '${output_vcf}'
]]>
</command>
<inputs>
<param name="reference_fasta" filename="reference_fasta.fa" type="data" format="fasta" label="Reference genome" help="Select the reference genome" />
<param name="input_bam" filename="input_bam.bam" type="data" format="bam" label="Input BAM file" help="Select the BAM file to analyze" />
<param name="dbsnp" type="data" filename="dbsnp.vcf" format="vcf" label="dbSNP VCF file" help="Select the dbSNP VCF file" />
<param name="emit_ref_confidence" type="select" label="Reference confidence mode" help="Select the mode for emitting reference confidence scores">
<option value="NONE">None</option>
<option value="BP_RESOLUTION">BP Resolution</option>
<option value="GVCF">GVCF</option>
</param>
<param name="max_alternate_alleles" type="integer" value="6" label="Maximum alternate alleles" help="Select the maximum number of alternate alleles to genotype" />
<param name="min_base_quality_score" type="integer" value="10" label="Minimum base quality" help="Minimum base quality required to consider a base for calling" />
</inputs>
<outputs>
<data name="output_vcf" format="vcf" label="${tool.name} on ${on_string}: GATK 4 VCF" />
</outputs>
<help>
**GATK 4 (Docker)**
docker pull seedgeorge/gatk4_and_bwa0.7.17_arm64 for ARM64 or broadinstitute/gatk:4.1.3.0 for AMD/Intel x86_64
This tool runs the Genome Analysis Toolkit (GATK) 4 in a Docker container.
For more information, consult the GATK documentation:
https://gatk.broadinstitute.org/hc/en-us
</help>
</tool>