--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin_dosage.xml	Wed Jul 06 07:05:15 2016 -0400
@@ -0,0 +1,77 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
+    <description>plugin genotype dosage</description>
+    <macros>
+        <token name="@EXECUTABLE@">dosage</token>
+        <token name="@PLUGIN_ID@">dosage</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@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+
+## Plugin section
+#set $section = $sec_plugin
+#if $section.tags:
+-- --tags "${section.tags}"
+#end if
+> "$output_file"
+
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <section name="sec_plugin" expanded="true" title="Plugin Options">
+            <param name="tags" type="text" value="" optional="true" label="VCF tag to determine the dosage from [PL,GL,GT]">
+                <validator type="regex" message="Tags  separated by commas">^(PL|GL|GT)(,(PL|GL|GT))*$</validator>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="#\[1]CHROM\t\[2]POS\t\[3]REF\t\[4]ALT\t\[5]A\t\[6]B"/>
+                    <has_text_matching expression="1\t3157410\tGA\tG\t2.0\t2.0"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>