# HG changeset patch
# User abretaud
# Date 1472656935 14400
# Node ID e978c66bb55f5e6be58da63879563a6f3dc315bb
# Parent  2e8e1bf4febf94ffed221c299cafaa1423e254be
Uploaded

diff -r 2e8e1bf4febf -r e978c66bb55f lordec_correct.xml
--- a/lordec_correct.xml	Mon Sep 28 13:19:01 2015 +0000
+++ b/lordec_correct.xml	Wed Aug 31 11:22:15 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="lordeccorrect" name="lordeccorrect" version="0.5.3">
+<tool id="lordeccorrect" name="lordeccorrect" version="0.6">
   <description>is an efficient tool for correcting sequencing errors in PacBio reads</description>
   <requirements>
-    <requirement type="package" version="0.5.3">lordec</requirement>
+    <requirement type="package" version="0.6">lordec</requirement>
   </requirements>
-  <command>
+  <command><![CDATA[
 lordec-correct
 -2 $short_reads
 -i $long_reads
@@ -16,8 +16,9 @@
 -b $advanced_options.branch
 -e $advanced_options.errorrate
 -T $advanced_options.threads
-#end if 
-2&gt;1
+#end if
+2>&1
+]]>
   </command>
 
   <inputs>
@@ -63,7 +64,7 @@
 
 **Integrated by**
 
-Yvan Le Bras and Cyril Monjeaud 
+Yvan Le Bras and Cyril Monjeaud
 
 GenOuest Bio-informatics Core Facility
 
@@ -77,6 +78,7 @@
 
   </help>
   <citations>
+    <citation type="doi">10.1186/s13742-015-0105-2</citation>
     <citation type="doi">10.1093/bioinformatics/btu538</citation>
     <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
     author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
@@ -86,5 +88,5 @@
     url = {https://www.e-biogenouest.org/resources/128},
     pages = {97-106}
     }</citation>
-</citations> 
+</citations>
 </tool>