--- a/deletion_predictor.xml	Wed Feb 11 09:26:43 2015 -0500
+++ b/deletion_predictor.xml	Thu Jun 04 17:52:04 2015 +0200
@@ -19,8 +19,8 @@
         <param name="bamfile" type="data" format="bam" label="input BAM file" />
     </repeat>
     <param name="covfile" type="data" format="bcf" label="BCF variant call file to extract coverage from" help="Use the Variant Calling tool to generate this file."/>
-    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="true" help="If selected, reads from different read groups will be treated strictly separate. If turned off, read groups with identical sample names are used together for identifying uncovered regions, but are still treated separately for the prediction of deletions." />
-    <param name="include_uncovered" type="boolean" label="include low-coverage regions" truevalue="-u" falsevalue="" checked="true" help="If selected, regions that fulfill the coverage criteria below, but are not statistically significant deletions, will be included in the output." />  
+    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="false" help="If selected, reads from different read groups will be treated strictly separate. If turned off, read groups with identical sample names are used together for identifying uncovered regions, but are still treated separately for the prediction of deletions." />
+    <param name="include_uncovered" type="boolean" label="include low-coverage regions" truevalue="-u" falsevalue="" checked="false" help="If selected, regions that fulfill the coverage criteria below, but are not statistically significant deletions, will be included in the output." />  
     <param name="max_cov" type="integer" value="0" label="maximal coverage allowed inside a low-coverage region (default: 0)" help="The maximal coverage at a site allowed to consider it as part of a low-coverage region" />
     <param name="min_size" type="integer" value="100" label="minimal deletion size (default: 100)" help="A low-coverage region must consist of at least this number of consecutive bases below the maximal coverage to consider it in further analyses."/>
   </inputs>