--- a/print_reads.xml	Tue Nov 26 06:10:20 2013 -0500
+++ b/print_reads.xml	Sat Nov 30 10:36:47 2013 -0500
@@ -73,7 +73,8 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
+    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" 
+        help="The input covariates table file which enables on-the-fly base quality score recalibration (intended for use with BaseRecalibrator files) (-BQSR,--BQSR)" />
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
@@ -212,7 +213,7 @@
 
 **Inputs**
 
-GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration CSV input files.
+GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration (gatk_report) input files.
 
 
 **Outputs**
@@ -235,7 +236,7 @@
  exception_if_no_tile           If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
  solid_recal_mode               How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
  solid_nocall_strategy          Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
- recal_file                     Filename for the input covariates table recalibration .csv file
+ recal_file                     Filename for the input covariates table recalibration .gatk_report file
  out                            The output BAM file
  bam_compression                Compression level to use for writing BAM files
  disable_bam_indexing           Turn off on-the-fly creation of indices for output BAM files.