--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_autosomal_recessive.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,70 @@
+<tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.0">
+    <description>Find variants meeting an autosomal recessive/dominant model</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        gemini 
+
+            #if $rec_or_dom == 'recessive':
+                ## start autosomal_recessive
+                autosomal_recessive
+            #else:
+                ## start autosomal_dominant
+                autosomal_dominant
+            #end if
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            #if $filter.filter_selector == 'yes':
+                --filter "${filter.filter}"
+            #end if
+
+            -d $d
+            #if int($min_kindreds) > 0:
+                --min-kindreds $min_kindreds
+            #end if
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+
+        <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
+            <option value="recessive">recessive</option>
+            <option value="dominant">dominant</option>
+        </param>
+
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+        <expand macro="min_sequence_depth" />
+        <param name="min_kindreds" size="4" type="integer" value="-1" lebel="The min. number of kindreds that must have a candidate variant in a gene"
+            help="-1 means default values (--min-kindreds)" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </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.
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>