--- a/print_reads.xml	Wed Feb 19 04:39:38 2014 -0500
+++ b/print_reads.xml	Mon Aug 25 17:43:11 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_print_reads" name="Print Reads" version="0.0.7">
+<tool id="gatk2_print_reads" name="Print Reads" version="@VERSION@.0">
   <description>on BAM files</description>
   <expand macro="requirements" />
   <macros>
@@ -32,11 +32,6 @@
    
     #include source=$standard_gatk_options#
     
-    #if str( $reference_source.reference_source_selector ) == "history":
-        -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
-    #end if
-    ##end standard gatk options
-    
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
@@ -202,7 +197,7 @@
 
 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal.  For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads.  Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
 
-For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html&gt;`_.
+For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_readutils_PrintReads.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;`_.
 
@@ -247,4 +242,5 @@
 
 @CITATION_SECTION@
   </help>
+  <expand macro="citations" />
 </tool>