# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1386707317 21600
# Node ID 39cb913568ec31e664748ed391e4208c25cbcb46
# Parent  f981ba577f2bf2e8f75e7daa2a241d5a0bc9be47
Do not select any annotations by default

diff -r f981ba577f2b -r 39cb913568ec snpEff.xml
--- a/snpEff.xml	Fri Nov 29 17:13:33 2013 -0600
+++ b/snpEff.xml	Tue Dec 10 14:28:37 2013 -0600
@@ -54,9 +54,9 @@
         #elif $snpDb.genomeSrc == 'history':
           -dataDir ${snpDb.snpeff_db.extra_files_path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
-            #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
+            #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
             #echo " "
-            #echo ' -'.join($annotations)
+            #echo ' -'.join($xannotations)
           #end if
           #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
             -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
@@ -174,12 +174,12 @@
 
         <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
             <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option>
-            <option value="-canon" selected="true">Only use canonical transcripts</option>
+            <option value="-canon">Only use canonical transcripts</option>
             <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
             <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
-            <option value="-lof" selected="true">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option>
+            <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option>
             <option value="-oicr">Add OICR tag in VCF file</option>
-            <option value="-onlyReg" selected="true">Only use regulation tracks</option>
+            <option value="-onlyReg">Only use regulation tracks</option>
             <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option>
         </param>
         <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>