--- a/gemini_interactions.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>Find genes among variants that are interacting partners</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">interactions</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command>
-<![CDATA[
-        gemini
-            --annotation-dir ${annotation_databases.fields.path}
-            #if $gene.gene_selector == 'lof':
-                ## lof interactions is a separate program
-                lof_interactions
-            #else:
-                ## use normal gemini interactions program
-                @BINARY@
-                -g "${gene.gene}"
-            #end if
-
-            -r "${radius}"
-            $variant_mode
-            "${ infile }"
-            > "${ outfile }"
-]]>
-    </command>
-    <inputs>
-        <expand macro="infile" />
-
-        <conditional name="gene">
-            <param name="gene_selector" type="select" label="Studying" help="">
-                <option value="gene">Interesting gene</option>
-                <option value="lof">All loss-of-function variants</option>
-            </param>
-            <when value="gene">
-                <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
-            </when>
-            <when value="lof"/>
-        </conditional>
-        <expand macro="annotation_dir" />
-        <expand macro="radius" />
-        <expand macro="variant_mode" />
-    </inputs>
-    <outputs>
-        <data name="outfile" format="tabular" />
-    </outputs>
-    <tests>
-        <test>
-        </test>
-    </tests>
-    <help>
-**What it does**
-
-Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
-Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the
-protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI.
-
-.. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627
-
-
-@CITATION@
-    </help>
-    <expand macro="citations">
-        <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
-    </expand>
-</tool>