--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_macros.xml	Fri Nov 29 09:27:22 2013 -0500
@@ -0,0 +1,45 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.4">snpEff</requirement>
+        </requirements>
+    </xml>
+  <xml name="stdio">
+    <conditional name="analysis_param_type">
+      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <yield />
+      </when>
+    </conditional>
+  </xml>
+  <xml name="reference_source_selector_param">
+    <stdio>
+        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+  </xml>
+  <token name="@EXTERNAL_DOCUMENTATION@">
+
+For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
+
+  </token>
+  <token name="@CITATION_SECTION@">------
+
+**Citation**
+
+For the underlying tool, please cite the following two publications:
+
+SnpEff citation:
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
+SnpSift citation:
+"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
+
+  </token>
+</macros>