# HG changeset patch
# User thanhlv
# Date 1558106368 14400
# Node ID bf0efbba5e8d7b23a14120697b1870d649b7eaed
# Parent  686ffd8c4f972cee260974b5e4f48427c6612b19
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/socru commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty

diff -r 686ffd8c4f97 -r bf0efbba5e8d macros.xml
--- a/macros.xml	Thu Feb 14 10:31:51 2019 -0500
+++ b/macros.xml	Fri May 17 11:19:28 2019 -0400
@@ -10,9 +10,9 @@
         <version_command>socru --version</version_command>
     </xml>
 
-    <!-- <xml name="citations">
+    <xml name="citations">
         <citations>
-            <citation type="doi">10.7717/peerj.5233</citation>
+            <citation type="doi">10.1101/543702</citation>
         </citations>
-    </xml> -->
+    </xml>
 </macros>
\ No newline at end of file
diff -r 686ffd8c4f97 -r bf0efbba5e8d socru.xml
--- a/socru.xml	Thu Feb 14 10:31:51 2019 -0500
+++ b/socru.xml	Fri May 17 11:19:28 2019 -0400
@@ -17,10 +17,13 @@
         --top_blast_hits top_blast_hits.tsv
         
         #if str($opt_args.max_bases_from_ends) != ""
-            --max_bases_from_ends $$opt_args.max_bases_from_ends
+            --max_bases_from_ends $opt_args.max_bases_from_ends
         #end if
         
-        --not_circular $opt_args.not_circular
+        #if $opt_args.not_circular
+            --not_circular
+        #end if
+
         --min_bit_score $opt_args.min_bit_score
         --min_alignment_length $opt_args.min_alignment_length
 
@@ -499,5 +502,5 @@
     
     Documentation can be found at `<https://github.com/quadram-institute-bioscience/socru>`_.
     ]]></help>
- <!-- <expand macro="citations" /> -->
+ <expand macro="citations" />
 </tool>