--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_autosomal_recessive.xml	Thu Feb 18 08:53:48 2016 -0500
@@ -0,0 +1,100 @@
+<tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.0">
+    <description>Find variants meeting an autosomal recessive/dominant model</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini
+
+            #if str($rec_or_dom) == 'recessive':
+                ## start autosomal_recessive
+                autosomal_recessive
+            #else:
+                ## start autosomal_dominant
+                autosomal_dominant
+            #end if
+
+            #if str($report.report_selector) != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
+            -d $d
+            #if int($min_kindreds) > 0:
+                --min-kindreds $min_kindreds
+            #end if
+
+            #if str($families).strip():
+                --families "$families"
+            #end if
+
+            $lenient
+            $allow_unaffected
+
+            #if int($min_gq) > 0:
+                --min-gq $min_gq
+            #end if
+
+            #if int($gt_pl_max) > -1:
+                --gt-pl-max $gt_pl_max
+            #end if
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+
+        <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
+            <option value="recessive">recessive</option>
+            <option value="dominant">dominant</option>
+        </param>
+
+        <expand macro="infile" />
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+        <expand macro="min_sequence_depth" />
+        <expand macro="family" />
+        <expand macro="lenient" />
+        <expand macro="unaffected" />
+        <expand macro="min_kindreds" />
+        <expand macro="min_gq" />
+        <expand macro="gt_pl_max" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_autosomal_input.db" ftype="gemini.sqlite" />
+            <param name="rec_or_dom" value="dominant" />
+            <param name="report_selector" value="column_filter" />
+            <param name="columns" value="gene,chrom,impact" />
+            <param name="lenient" value="true" />
+            <output name="outfile" file="gemini_autosomal_dominant_result.tabular" />
+        </test>
+        <test>
+            <param name="infile" value="gemini_autosomal_input.db" ftype="gemini.sqlite" />
+            <param name="rec_or_dom" value="recessive" />
+            <param name="report_selector" value="column_filter" />
+            <param name="columns" value="gene,chrom,impact" />
+            <param name="lenient" value="true" />
+            <output name="outfile" file="gemini_autosomal_recessive.tabular" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a
+built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern.
+The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts.
+
+    </help>
+    <expand macro="citations"/>
+</tool>