# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1373263838 18000
# Node ID 630532975fa935043f45592b88856f2f66925173
# Parent  239e200ae99f7de7dc7028858e33a44d7840e948
Fix more typos

diff -r 239e200ae99f -r 630532975fa9 shear_sv.xml
--- a/shear_sv.xml	Sat Jul 06 04:51:48 2013 -0500
+++ b/shear_sv.xml	Mon Jul 08 01:10:38 2013 -0500
@@ -11,12 +11,12 @@
   <!--
   <version_command></version_command>
   -->
-  <command>java -jar  \$SHEAR_JAR_PATH/SHEAR.jar sv -r $prefix 
+  <command>java -jar  \$SHEAR_JAR_PATH/SHEAR.jar sv -p $prefix 
      -b $bamfile 
      #if $genomeSource.refGenomeSource == 'indexed':
        -f $genomeSource.ref_fastas.fields.path 
        -i $genomeSource.bwa_indices.fields.path 
-       -t $genomeSource.twobit_indices.fields.paths
+       -t $genomeSource.twobit_indices.fields.path
      #else:
        -f $genomeSource.ref_fasta
        -i $genomeSource.bwa_index