--- a/gemini_annotate.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>adding your own custom annotations</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">annotate</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <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>
-    <inputs>
-        <expand macro="infile" />
-        <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/>
-
-        <param name="column_name" 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" />
-    </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>