--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_pathways.xml	Tue Dec 29 10:22:42 2015 -0500
@@ -0,0 +1,56 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Map genes and variants to KEGG pathways</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">pathways</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini
+            #if $annotation_databases:
+                --annotation-dir ${annotation_databases.fields.path}
+            #end if
+            @BINARY@
+            -v $ensembl
+            $lof
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+
+        <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use"
+            help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
+            <validator type="in_range" min="66" max="71"/>
+        </param>
+
+        <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
+            label="Report only pathways with loss-of-function variants" help="(--lof)"/>
+        <expand macro="annotation_dir" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
+            <param name="ensembl" value="68" />
+            <output name="outfile" file="gemini_pathways_result.tabular" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
+Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
+We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
+
+This requires your VCF be annotated with either snpEff/VEP.
+
+    </help>
+    <expand macro="citations"/>
+</tool>