--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_interactions.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,68 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Find genes among variants that are interacting partners</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">interactions</token>
+    </macros>
+    <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 }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <conditional name="gene">
+            <param name="gene_selector" type="select" label="Studying" help="">
+                <option value="gene">Interesting gene</option>
+                <option value="lof">All loss-of-function variants</option>
+            </param>
+            <when value="gene">
+                <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
+            </when>
+            <when value="lof"/>
+        </conditional>
+        <expand macro="annotation_dir" />
+        <expand macro="radius" />
+        <expand macro="variant_mode" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </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>