# HG changeset patch
# User sanbi-uwc
# Date 1504856258 14400
# Node ID 58b5fe349997a8bb415e496df90a91e1c07cc2ed
# Parent  a269ca0887737dfadcee0dd41831125e92daa694
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 3b4561ab40c1f62ce735c46e57f029cf48f2074e-dirty

diff -r a269ca088773 -r 58b5fe349997 lofreq_call.xml
--- a/lofreq_call.xml	Thu Sep 07 05:51:31 2017 -0400
+++ b/lofreq_call.xml	Fri Sep 08 03:37:38 2017 -0400
@@ -63,7 +63,6 @@
 
         <param name="BaseAlignmentAndIndedAlignment" type="select" display="checkboxes" multiple="true" label="Base-alignment (BAQ) and indel-aligment (IDAQ) qualities Options">
             <option value="--no-baq">Disable use of base-alignment quality (BAQ)</option>
-            <option value="--no-idaq">Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)</option>
             <option value="--del-baq">Delete pre-existing BAQ values, i.e. compute even if already present in BAM</option>
             <option value="--no-ext-baq"> Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)</option>
         </param>
@@ -90,7 +89,6 @@
             <option value="--no-default-filter">Don't run default 'lofreq filter' automatically after calling variants</option>
             <option value="--force-overwrite">Overwrite any existing output</option>
             <option value="--verbose">Be verbose</option>
-            <option value="--debug">Enable debugging</option>
         </param>
 
     </inputs>