--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jul 10 13:36:24 2018 -0400
@@ -0,0 +1,57 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">varscan</requirement>
+            <requirement type="package" version="4.2.1">gawk</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@VERSION@">2.4.3</token>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
+            <regex match=".*" source="both" level="log" description="tool progress"/>
+        </stdio>
+        <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/gr.129684.111</citation>
+        </citations>
+    </xml>
+
+    <xml name="min_coverage">
+        <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
+            label="Minimum read depth" help="Minimum depth at a position to make a call"/>
+    </xml>
+    <xml name="min_reads2">
+        <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
+            label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
+    </xml>
+    <xml name="min_avg_qual">
+        <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
+            label="Minimum base quality at a position to count a read"/>
+    </xml>
+    <xml name="min_var_freq" token_value="0.01">
+        <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
+            label="Minimum variant allele frequency threshold"/>
+    </xml>
+    <xml name="min_freq_for_hom">
+        <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
+            label="Minimum frequency to call homozygote"/>
+    </xml>
+    <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01">
+        <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0"
+            label="@LABEL@"/>
+    </xml>
+    <xml name="strand_filter">
+        <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
+            <option value="no" selected="True">no</option>
+            <option value="yes">yes</option>
+        </param>
+    </xml>
+
+</macros>