# HG changeset patch
# User david-hoover
# Date 1348151668 14400
# Node ID 4fa715d44c26a4c8a6340e04dd8b915656aa27bd
# Parent  77c0583db74fe4348183b8d7e821a5a79ad96d46
Uploaded

diff -r 77c0583db74f -r 4fa715d44c26 print_reads.xml
--- a/print_reads.xml	Thu Sep 20 10:08:03 2012 -0400
+++ b/print_reads.xml	Thu Sep 20 10:34:28 2012 -0400
@@ -21,7 +21,7 @@
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
-    --recal_file "${input_recal}"
+    --BQSR "${input_recal}"
     --disable_bam_indexing
    '
     ##start standard gatk options
@@ -120,7 +120,7 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
+    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
         <option value="cached">Locally cached</option>