<tool id="cfsan_snp_pipeline_merge_vcfs" name="CFSAN SNP Pipeline: merge vcfs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>from multiple samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.vcf'
#for $input_vcf in $input_vcf_collection
    -n '$input_vcf.element_identifier' -f '$input_vcf'
#end for
> ./file &&
cfsan_snp_pipeline merge_vcfs ./file &&
mv snpma.vcf '$output'
    ]]></command>
    <inputs>
        <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
    </inputs>
    <outputs>
        <data name="output" label="SNP matrix" format="vcf"/>
    </outputs>
    <tests>
        <test>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="sample1" value="samples/sample1/consensus.vcf" ftype="vcf"/>
                    <element name="sample2" value="samples/sample2/consensus.vcf" ftype="vcf"/>
                    <element name="sample3" value="samples/sample3/consensus.vcf" ftype="vcf"/>
                    <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/>
                </collection>
            </param>
            <output name="output" ftype="vcf">
                <assert_contents>
                    <has_size value="31888" delta="100"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Merges the consensus vcf files from all samples into a single multi-vcf file.

**More information**

CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
    ]]></help>
    <expand macro="citations"/>
</tool>