--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_gene_wise.xml	Tue Feb 16 05:55:08 2016 -0500
@@ -0,0 +1,63 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Custom genotype filtering by gene</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">gene_wise</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            
+            #if int($min_filters) > 0:
+                --min_filters $min_filters
+            #end if
+
+            #if $gt_filter.strip():
+                --gt-filter "${gt_filter}"
+            #end if
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+
+        <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filter)">
+            <expand macro="sanitize_query" />
+        </param>
+        <param name="min_filters" type="integer" value="0" min="0" label="Minimum number of filters" help="(--min-filters)" />
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
+            <param name="gt_filter" value="((gt_depths).(*).(>=1).(all))" />
+            <output name="outfile" file="gemini_gene_wise_result.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools.
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>