--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin_mendelian.xml	Wed Jul 06 07:06:58 2016 -0400
@@ -0,0 +1,143 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
+    <description>plugin Count Mendelian consistent / inconsistent genotypes</description>
+    <macros>
+        <token name="@EXECUTABLE@">mendelian</token>
+        <token name="@PLUGIN_ID@">mendelian</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 $section.trios.trios_src == 'trio':
+  --trio "${section.trios.mother},${section.trios.father},${section.trios.child}"
+#elif $section.trios.trios_src == 'trio_file':
+  --trio-file "$section.trios.trio_file"
+#end if
+#if $section.mode:
+ #set $modes =  str($section.mode).split(',')
+ #if 'count' in $modes:
+  --count
+ #end if
+ #if 'delete' in $modes:
+  --delete
+ #end if
+ #if '+' in $modes:
+  --list '+'
+ #end if
+ #if 'x' in $modes:
+  --list x
+ #end if
+#end if
+2> tmp_stderr
+> "$output_file"
+&& cat tmp_stderr
+]]>
+</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">
+            <!-- trios -->
+            <conditional name="trios">
+                <param name="trios_src" type="select" label="Sample relationship">
+                    <option value="trio">trio - mother,father,child</option>
+                    <option value="trio_file">trios file</option>
+                </param>
+                <when value="trio">
+                   <param name="mother" type="text" value="" label="name of mother"/>
+                   <param name="father" type="text" value="" label="name of father"/>
+                   <param name="child" type="text" value="" label="name of child"/>
+                </when>
+                <when value="trio_file">
+                    <param name="trio_file" type="data" format="txt" label="Trio File" help="List of trios, one per line" />
+                </when>
+            </conditional>
+            <param name="mode" type="select" label="Action" multiple="true" min="1">
+                <option value="count">count the number of consistent sites</option>
+                <option value="delete">delete inconsistent genotypes (set to './.')</option>
+                <option value="+">consistent sites (+)</option>
+                <option value="x">inconsistent sites (x)</option>
+            </param>
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- This is just a test on a random file, should have a real test case -->
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="trios_src" value="trio" />
+            <param name="mother" value="NA00001" />
+            <param name="father" value="NA00002" />
+            <param name="child" value="NA00006" />
+            <param name="mode" value="delete" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="2698758" />
+                    <not_has_text text="2698769" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- This is just a test on a random file, should have a real test case -->
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="trios_src" value="trio" />
+            <param name="mother" value="NA00001" />
+            <param name="father" value="NA00002" />
+            <param name="child" value="NA00006" />
+            <param name="mode" value="x" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <not_has_text text="2698758" />
+                    <has_text text="2698769" />
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
+
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>