--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/6_merge_vcfs.xml	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,42 @@
+<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="1.3.1">bcftools</requirement>
+        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package">tabix</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        $__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>
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