--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_region.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,75 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Extracting variants from specific regions or genes</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">region</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            #if $region.region_selector == '--reg':
+                #if str(${region.region}) != '':
+                    --reg "${region.region}"
+                #end if
+            #else:
+                #if str(${region.gene}) != '':
+                    --gene "${region.gene}"
+                #end if
+            #end if
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            #if $filter.filter_selector == 'yes':
+                --filter "${filter.filter}"
+            #end if
+
+            $header
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <conditional name="region">
+            <param name="region_selector" type="select" label="Select by ...?" help="">
+                <option value="--reg">genomic coordinates</option>
+                <option value="--gene">gene name</option>
+            </param>
+            <when value="--reg">
+                <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
+            </when>
+            <when value="--gene">
+                <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
+            </when>
+        </conditional>
+
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+
+
+        <expand macro="add_header_column" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+One often is concerned with variants found solely in a particular gene or genomic region.
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>