# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1356717020 21600
# Node ID 6e641ee0285166b9b91c4396634abbfa73e05b70
# Parent  3924f62cd4e75528e3b7474e01cf65b0f65c675b
Fix base_recalibrator.xml option: no_standard_covs

diff -r 3924f62cd4e7 -r 6e641ee02851 base_recalibrator.xml
--- a/base_recalibrator.xml	Fri Dec 28 11:21:40 2012 -0600
+++ b/base_recalibrator.xml	Fri Dec 28 11:50:20 2012 -0600
@@ -167,7 +167,7 @@
         </param>
       </when>
     </conditional>
-    <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" />
+    <param name="standard_covs" type="boolean" truevalue="" falsevalue="--no_standard_covs" checked="false" label="Do not use the standard set of covariates in addition to the ones selected" help="--no_standard_covs/-noStandard" />
     <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
       <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
       <option value="ReadGroupCovariate" />