--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/HGVSAnnotation.xml	Wed Mar 25 16:00:12 2015 -0600
@@ -0,0 +1,46 @@
+<?xml version="1.0"?>
+
+<tool id="hgvs_annotation_1" name="Functionally 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 change prediction, gene names, pathways, etc.</description>
+  <version_string>hgvs_table_annotate -v</version_string>
+  <command interpreter="perl">hgvs_table_annotate $__tool_data_path__ -q sift/$sift_dir polyphen2/$polyphen_file\.txt.gz gerp/$gerp_dir TissueDistributionDBs/$tissue_dist_file\.tab pathways/$pathways_file\.txt $refFlat_bed $input_hgvs_table $out_hgvs_annotated_table $keep_synonymous</command>
+  <inputs>
+    <param format="achri_snp_table" name="input_hgvs_table" type="data" label="Variant calls table with HGVS syntax"/>
+    <param name="keep_synonymous" type="boolean" label="Report synonymous variants?" default="false" truevalue="true" falsevalue="false"/>
+    <param name="sift_dir" type="select" display="radio" dynamic_options="SIFT_fileOptions()" label="SIFT precalculated tables" help="SIFT scores below 0.05 generally indicate a harmful variant"/>
+    <param name="polyphen_file" type="select" display="radio" dynamic_options="PolyPhen_fileOptions()" label="PolyPhen2 precalculated tables" help="Makes a call of deleterious, possibly deleterious, or benign"/>
+    <param name="gerp_dir" type="select" display="radio" dynamic_options="GERP_fileOptions()" label="GERP precalculated tables" help="GERP scores far from zero generally indicate a harmful variant"/>
+    <param name="tissue_dist_file" type="select" display="radio" dynamic_options="TissueDist_fileOptions()" label="Gene tissue distribution DB" help="Lists in descending order the major tissue types in which each gene is expressed"/>
+    <!--<param name="pseudogene_file" type="select" display="radio" dynamic_options="Pseudogene_fileOptions()" label="Pseudogene DB" help="Genes with pseudogenes are more likely to generate variant false positives through mismapping"/>-->
+    <param name="pathways_file" type="select" display="radio" dynamic_options="Pathway_fileOptions()" label="Biochemical Pathway DB" help="Gives an idea of processes in which the gene is involved"/>
+    <param name="refFlat_bed" type="data" format="bed" label="Gene Names DB" help="Import a refFlat file from the 'Genomic coding sequence regions' folder under Shared Data. Alternatively, provide a BED format file which defined exons and has the gene name in the 4th column"/>
+  </inputs>
+  <outputs>
+    <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Functionally annotated HGVS variant table"/>
+  </outputs>
+
+  <!-- the following code populates the dbSNP selection from the public dbSNP datasets available in the local Galaxy installation -->
+  <code file="sift_datasets.py"/>
+  <code file="polyphen_datasets.py"/>
+  <code file="gerp_datasets.py"/>
+  <code file="tissuedist_datasets.py"/>
+  <!-- <code file="pseudogene_datasets.py"/>-->
+  <code file="pathways_datasets.py"/>
+
+  <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>