diff depth_of_coverage.xml @ 6:b80301676614 draft

Uploaded

--- a/depth_of_coverage.xml	Tue Mar 11 07:42:09 2014 -0400
+++ b/depth_of_coverage.xml	Wed Feb 18 11:36:59 2015 -0500
@@ -1,6 +1,7 @@
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.7">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
   <description>on BAM files</description>
   <expand macro="requirements" />
+  <expand macro="version_command" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
@@ -692,7 +693,7 @@
 
 DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. 
 
-For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html&gt;`_.
+For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html&gt;`_.
 
 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
 
@@ -738,4 +739,5 @@
 
 @CITATION_SECTION@
   </help>
+  <expand macro="citations" />
 </tool>