--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_annotate.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,96 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>adding your own custom annotations</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">annotate</token>
+    </macros>
+    <command>
+<![CDATA[
+
+bgzip -c $annotate_source > tabixed.gz;
+tabix -p bed tabixed.gz;
+
+        gemini @BINARY@
+            -f tabixed.gz
+            -c $column_name
+            -a $a.a_selector
+            #if $a.a_selector == 'extract':
+                -t $a.column_type
+                -e $a.column_extracts
+                -o $a.operation
+            #end if
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/>
+
+        <param name="column_name" size="20" type="text" value=""
+            label="The name of the column to be added to the variant table" help="(-c)">
+            <sanitizer invalid_char=" ">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" /> 
+                </valid>
+            </sanitizer>
+        </param>
+        <conditional name="a">
+            <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
+                <option value="boolean">Did a variant overlap a region or not? (boolean)</option>
+                <option value="count">How many regions did a variant overlap? (count)</option>
+                <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option>
+            </param>
+            <when value="extract">
+
+                <param name="column_extracts" label="Column to extract information from for list annotations" 
+                    type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/>
+
+
+                <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
+                    help="(-t)">
+                    <option value="float">Decimal precision number (float)</option>
+                    <option value="integer">Integer number (integer)</option>
+                    <option value="text">Text columns such as “valid”, “yes” (text)</option>
+                </param>
+
+                <param name="operation" type="select" label="Operation to apply to the extract column values ..."
+                    help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)">
+                    <option value="mean">Compute the average of the (numeric) values</option>
+                    <option value="median">Compute the median of the (numeric) values</option>
+                    <option value="mix">Compute the minimum of the (numeric) values</option>
+                    <option value="max">Compute the maximum of the (numeric) values</option>
+                    <option value="mode">Compute the maximum of the (numeric) values</option>
+                    <option value="first">Use the value from the first record in the annotation file</option>
+                    <option value="last">Use the value from the last record in the annotation file</option>
+                    <option value="list">Create a comma-separated list of the observed (text) values</option>
+                    <option value="uniq_list">Create a comma-separated list of non-redundant observed (text) values</option>
+                </param>
+
+            </when>
+            <when value="boolean"/>
+            <when value="count"/>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+It is inevitable that researchers will want to enhance the gemini framework with their own, custom annotations. gemini provides a sub-command called annotate for exactly this purpose.
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>