diff lordec_trim.xml @ 6:d135caa42d04 draft

Uploaded

--- a/lordec_trim.xml	Wed Aug 31 11:22:34 2016 -0400
+++ b/lordec_trim.xml	Wed Aug 31 11:22:43 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="lordectrim" name="lordectrim" version="0.5.3">
+<tool id="lordectrim" name="lordectrim" version="0.5.3.1">
   <description>is an efficient tool to trim weak regions of PacBio corrected reads</description>
   <requirements>
-    <requirement type="package" version="0.5.3">lordec</requirement>
+    <requirement type="package" version="0.6">lordec</requirement>
   </requirements>
-  <command>
+  <command><![CDATA[
 #if $split
 lordec-trim-split
 #else
@@ -11,6 +11,7 @@
 #end if
 -i $long_reads
 -o $corrected_read_file
+]]>
 </command>
 
   <inputs>
@@ -39,7 +40,7 @@
 
 **Integrated by**
 
-Yvan Le Bras and Cyril Monjeaud 
+Yvan Le Bras and Cyril Monjeaud
 
 GenOuest Bio-informatics Core Facility
 
@@ -53,6 +54,7 @@
 
   </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.},
@@ -62,5 +64,5 @@
     url = {https://www.e-biogenouest.org/resources/128},
     pages = {97-106}
     }</citation>
-</citations> 
+</citations>
 </tool>