<tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
    <description>into a multi-sample VCF with consensus SNPs</description>
    <requirements>
        <requirement type="package" version="1.6">bcftools</requirement>
        <requirement type="package" version="1.0.6">bzip2</requirement>
        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
        <requirement type="package" version="0.2.5">tabix</requirement>
        <requirement type="package" version="3.5">python</requirement>
        <requirement type="package" version="1.6">htslib</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
        env &&
        ls -lah \$CONDA_DEFAULT_ENV/bin &&
        ls -lah \$CONDA_DEFAULT_ENV/lib &&
        python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
            #for $vcf in $vcfs
                -n $vcf.element_identifier -f $vcf
            #end for
        > ./file
        && cat ./file
        && cfsan_snp_pipeline merge_vcfs ./file
    ]]></command>
    <inputs>
        <param type="data_collection" format="vcf" collection_type="list" name="vcfs" label="List of VCFs" />
    </inputs>
    <outputs>
        <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
    </outputs>
    <tests>
        <test>
            <param name="vcfs">
                <collection type="list">
                    <element name="sample1" value="samples/sample1/consensus.vcf" />
                    <element name="sample2" value="samples/sample2/consensus.vcf" />
                    <element name="sample3" value="samples/sample3/consensus.vcf" />
                    <element name="sample4" value="samples/sample4/consensus.vcf" />
                </collection>
            </param>
            <output name="snpmav" value="snpma.vcf" lines_diff="2" />
        </test>
    </tests>
    <help><![CDATA[
        <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
    ]]></help>
    <citations>
        <citation type="doi">10.7717/peerj-cs.20</citation>
    </citations>
</tool>