--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PoorGeneCoverage.xml	Wed Mar 25 15:49:28 2015 -0600
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+
+<tool id="poor_gene_coverage" name="Report Poor Coverage">
+  <description>regions for a set of genes</description>
+  <version_string>echo 1.0.0</version_string>
+  <command interpreter="perl">annotate_low_coverage $__tool_data_path__  ${captureKitRegions} $poorCaptureRegions $outputTable 
+     #if $targetGenes.dataset and str($targetGenes) > '':
+       $targetGenes 
+     #else:
+       /dev/null
+     #end if
+     NM_
+  </command>
+  <inputs>
+    <param name="sampleName" type="text" label="Biological sample name" help="Will be used to name the output files"/>
+    <param name="captureKitRegions" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
+    <param format="bed" name="poorCaptureRegions" type="data" label="BED file of low coverage regions"/>
+    <param format="text" name="targetGenes" type="data" optional="true" label="List of genes to report, one per line"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="outputTable"/>
+  </outputs>
+
+  <!-- the following code populates the  selection from the public capture kit BED datasets available in the local Galaxy installation -->
+  <code file="capture_kits.py"/>
+  <tests/>
+
+  <help>This tools summarized low coverage regions on a per gene basis, including information on clinically relevant variants (according to ClinVar) that might have been missed</help>
+
+</tool>