--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AnnotateVariants.xml	Wed Mar 25 13:10:47 2015 -0600
@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+
+<tool id="hgvs_annotation_2" name="Annotate an HGVS table">
+  <requirements>
+    <requirement type="package">genesplicer</requirement>
+	    <requirement type="package">human</requirement>
+		    <requirement type="package">score3.pl</requirement>
+			    <requirement type="package">score5.pl</requirement>
+  </requirements>
+
+  <description>with deleterious AA and splicing change predictions, protein domain disruptions, etc.</description>
+  <version_string>hgvs_table_annotate -v</version_string>
+  <command interpreter="perl">hgvs_table_annotate $__tool_data_path__ -q /sift/hg19 /polyphen2/hg19.txt.gz /dbs/gerp/hg19 /dbs/TissueDistributionDBs/human.v2009-07-30.tab /dbs/pathways/KEGG.human.2012-09-25.txt /dbs/interpro_supermatch_hg19.bed /dbs/OMIM/morbidmap $input_hgvs_table $out_hgvs_annotated_table /hg19.fa</command>
+  <inputs>
+    <param format="achri_snp_table" name="input_hgvs_table" type="data" label="Variant calls table with HGVS syntax"/>
+  </inputs>
+  <outputs>
+    <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Functionally annotated HGVS variant table"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help>
+This tool reports several functional attributes, and potential for functional disturbance, based on genes that have declared sequence variants. 
+These results can be used to help find the genetic cause of a clinical phenotype.
+  </help>
+
+</tool>