<tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
    <description>from multiple samples</description>
    <requirements>
        <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
        <!-- <requirement type="package" version="2.4.5">bowtie2</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="1.0.8">bzip2</requirement>
        <requirement type="package" version="2.2.1">snp-pipeline</requirement> -->
        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
        python $__tool_directory__/snp-wind.py ./
                #for $call in $calls
                    -n $call.element_identifier -f $call
                #end for
        -p "var.fit.vcf" > ./file
        && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist
    ]]></command>
    <inputs>
        <param type="data_collection" name="calls" format="vcf" collection_type="list" />
    </inputs>
    <outputs>
        <data name="snplist" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="calls">
                <collection type="list">
                    <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" ftype="fastqsanger" />
                    <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" />
                    <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" />
                    <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" />
                </collection>
            </param>
            <output name="snplist" value="snplist.txt" />
        </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>