--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DepthReports.xml	Wed Mar 25 13:31:40 2015 -0600
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+
+<tool id="depth_reports_1" name="Compute depth of sequencing coverage">
+  <description>over targeted regions in a genome</description>
+  <version_string>depth_reports -v</version_string>
+  <command interpreter="perl">depth_reports $__tool_data_path__ -q $input_bam ${target_bed}.bed $out_summary_table $out_poor_coverage_bed $out_depth_graph $out_depth_table $out_mapped_percentile_table $dud_bed</command>
+  <inputs>
+    <param format="bam" name="input_bam" type="data" label="Mapped alignment file"/>
+    <param name="target_bed" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
+    <param format="bed" name="dud_bed" type="data" label="Targeted regions to ignore (known duds)" optional="true" default="/dev/null"/>
+  </inputs>
+  <outputs>
+    <data name="out_summary_table" format="achri_depth_summary_table" label="Depth of coverage summary (mean, median, etc.)"/>
+    <data name="out_poor_coverage_bed" format="bed" label="Low coverage targeted regions"/>
+    <data name="out_depth_graph" format="png" label="Cumulative depth of coverage graph"/>
+    <data name="out_depth_table" format="tabular" label="Number of bases at each depth of coverage"/>
+    <data name="out_mapped_percentile_table" format="tabular" label="Mapped read depth percentiles"/>
+  </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>
+    <test>
+     <param name="input_bam" value="depth_test.bam" ftype="bam"/>
+     <param name="target_bed" value="brcas.bed" ftype="bed"/>
+     <output name="out_summary_table">
+       <assert_contents>
+         <has_text text="targeted nucleotide bases: 155091"/>
+         <has_text text="bases mapped to targeted regions: 11473773"/>
+         <has_text text="bases with less than 20-fold coverage: 19046"/>
+       </assert_contents>
+     </output>
+     <output name="out_depth_graph" ftype="png"/>
+    </test>
+  </tests>
+
+  <help>
+This tool reports several statistics describing the depth of coverage of a next-gen sequencing run over its targeted reference genome. 
+These results can be used to assess the quality of the sequencing for SNP calls, etc.
+  </help>
+
+</tool>