# HG changeset patch
# User rnateam
# Date 1523366332 14400
# Node ID 9769fa6f0afb1d490585c42a9951a51880b67bb1
# Parent  91b70feb0cfaf2c6b80781dd6601bbb3aa4cf23b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 9f58716ffd4e4e223d37046318818c39338c4880

diff -r 91b70feb0cfa -r 9769fa6f0afb intarna.xml
--- a/intarna.xml	Fri Mar 23 17:56:31 2018 -0400
+++ b/intarna.xml	Tue Apr 10 09:18:52 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="intarna" name="IntaRNA" version="2.1.0.1">
+<tool id="intarna" name="IntaRNA" version="2.1.0.2">
     <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
     <macros>
         <macro name="query_macro">
@@ -128,7 +128,7 @@
                 #end if
 
                 ## Seed param.
-                --noSeed $advancedOptions.seed.noSeed
+                $advancedOptions.seed.noSeed
                 --seedBP $advancedOptions.seed.seedBP
                 --seedMaxUP $advancedOptions.seed.seedMaxUP
                 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
@@ -185,7 +185,7 @@
                 --tAccL $advancedOptions.target.tAccL
 
                 ## Seed param.
-                --noSeed $advancedOptions.seed.noSeed
+                $advancedOptions.seed.noSeed
                 --seedBP $advancedOptions.seed.seedBP
                 --seedMaxUP $advancedOptions.seed.seedMaxUP
 
diff -r 91b70feb0cfa -r 9769fa6f0afb test-data/intarna_result.tabular
--- a/test-data/intarna_result.tabular	Fri Mar 23 17:56:31 2018 -0400
+++ b/test-data/intarna_result.tabular	Tue Apr 10 09:18:52 2018 -0400
@@ -1,5 +1,4 @@
 id1	start1	end1	id2	start2	end2	subseqDP	hybridDP	E
 mRNA1	85	95	ncRNA1	21	32	GUGGUGAGGAG&CUCCUCACACAC	(((((((((((&)))))))).)))	-12.0345
-mRNA1	127	135	ncRNA2	18	25	GGCACCUGC&GCAGGGCC	(((.(((((&))))))))	-7.20671
+mRNA1	52	58	ncRNA2	28	34	UCAGUUA&UGACUGA	(((((((&)))))))	-3.32148
 mRNA2	86	97	ncRNA1	20	31	UGUGUGACGAGU&ACUCCUCACACA	(((((((.((((&)))).)))))))	-8.33678
-mRNA2	15	18	ncRNA2	22	25	GGCC&GGCC	((((&))))	-5.12558