# HG changeset patch
# User yboursin
# Date 1477054283 14400
# Node ID 67c078448bea74fce240f954deacf0c1e26107c1
# Parent  73a9e9df80da9234ff0ea4d96635fc52159f4bbe
Uploaded

diff -r 73a9e9df80da -r 67c078448bea README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Oct 21 08:51:23 2016 -0400
@@ -0,0 +1,1 @@
+EBA2016-v1  RSEM v 1.2.28
diff -r 73a9e9df80da -r 67c078448bea rsem_prepare_reference.xml
--- a/rsem_prepare_reference.xml	Wed May 25 10:08:02 2016 -0400
+++ b/rsem_prepare_reference.xml	Fri Oct 21 08:51:23 2016 -0400
@@ -12,16 +12,13 @@
     rsem-prepare-reference 
     #if $polya.polya_use == 'add':
       #if $polya.polya_length:
-        --polyA-length $polya.polya_length
+        --polyA --polyA-length $polya.polya_length
       #end if
     #elif $polya.polya_use == 'subset':
       --no-polyA-subset $polya.no_polya_subset
       #if $polya.polya_length:
         --polyA-length $polya.polya_length
       #end if
-    #elif $polya.polya_use == 'none':
-      --no-polyA
-    #end if
     $ntog
     $bowtie
     $bowtietwo
@@ -75,9 +72,9 @@
     </param>
     <conditional name="polya">
       <param name="polya_use" type="select" label="PolyA ">
-        <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
+        <option value="add">Add poly(A) tails to all transcripts</option>
         <option value="subset">Exclude poly(A) tails from selected transcripts</option>
-        <option value="none">Do not add poly(A) tails to any transcripts</option>
+        <option value="none" selected="true">Do not add poly(A) tails to any transcripts</option>
       </param>
       <when value="add">
         <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">