diff lordec_graph.xml @ 4:f0b144292846 draft

Uploaded

--- a/lordec_graph.xml	Wed Aug 31 11:22:15 2016 -0400
+++ b/lordec_graph.xml	Wed Aug 31 11:22:26 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="lordecgraph" name="lordec_graph" version="0.5.3">
+<tool id="lordecgraph" name="lordec_graph" version="0.6">
   <description>is an efficient tool to generate de Bruijn graph from 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[
 lordec-build-SR-graph
 -2 $short_reads
 -k $kmer_len
@@ -11,8 +11,9 @@
 -g $outgraph
 #if str( $advanced_options.advanced_options_selector) == "advanced"
 -T $advanced_options.threads
-#end if 
-2&gt;1
+#end if
+2>&1
+]]>
   </command>
 
   <inputs>
@@ -55,7 +56,7 @@
 
 **Integrated by**
 
-Yvan Le Bras and Cyril Monjeaud 
+Yvan Le Bras and Cyril Monjeaud
 
 GenOuest Bio-informatics Core Facility
 
@@ -69,6 +70,7 @@
 
   </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.},
@@ -78,5 +80,5 @@
     url = {https://www.e-biogenouest.org/resources/128},
     pages = {97-106}
     }</citation>
-</citations> 
+</citations>
 </tool>