--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin_missing2ref.xml	Wed Jul 06 07:07:16 2016 -0400
@@ -0,0 +1,81 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
+    <description>plugin Set missing genotypes</description>
+    <macros>
+        <token name="@EXECUTABLE@">missing2ref</token>
+        <token name="@PLUGIN_ID@">missing2ref</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILE@
+#set $section = $sec_restrict
+@PREPARE_TARGETS_FILE@
+
+bcftools plugin @EXECUTABLE@
+
+## VCF input section
+#set $section = $sec_restrict
+@INCLUDE@
+@EXCLUDE@
+@REGIONS@
+@TARGETS@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+
+## Plugin section
+#set $section = $sec_plugin
+#if $section.phased or $section.major:
+--
+${section.phased}
+${section.major}
+#end if
+> "$output_file"
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <section name="sec_plugin" expanded="true" title="Plugin Options">
+            <param name="phased" type="boolean" truevalue="--phased" falsevalue="" checked="false" label="Phased" help="Set to 0|0" />
+            <param name="major" type="boolean" truevalue="--major" falsevalue="" checked="false" label="Major" help="Set to major allele" />
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="0/0:245" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>