--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/4_merge_sites.xml	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,41 @@
+<tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
+    <description>from multiple samples</description>
+    <requirements>
+        <requirement type="package" version="2.2.6">bowtie2</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package">snp-pipeline</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        $__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" />
+                    <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" />
+                    <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" />
+                    <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" />
+                </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>
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