# HG changeset patch
# User rnateam
# Date 1485038334 18000
# Node ID 433601e9f132796b553a6e045455ac9076989be8
# Parent b06dc2bb3716e6767338f5ca80b0d69cba7abdca
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
diff -r b06dc2bb3716 -r 433601e9f132 locarna_pairwise.xml
--- a/locarna_pairwise.xml Fri Jan 13 16:49:33 2017 -0500
+++ b/locarna_pairwise.xml Sat Jan 21 17:38:54 2017 -0500
@@ -48,6 +48,10 @@
@HEURISTIC_ARGS@
+ #if str($alignment_mode.alignment_mode_selector) == "sparse"
+ @HEURISTIC_SPARSE_ARGS@
+ #end if
+
@CONSTRAINT_ARGS@
## -------------------- output
@@ -93,7 +97,7 @@
-
+
@@ -119,7 +123,13 @@
-
+
+
+
+
+
diff -r b06dc2bb3716 -r 433601e9f132 macros.xml
--- a/macros.xml Fri Jan 13 16:49:33 2017 -0500
+++ b/macros.xml Sat Jan 21 17:38:54 2017 -0500
@@ -141,6 +141,12 @@
#end if
+
+ --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
+ --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
+
+
+
## -------------------- constraint parameters
$Constraints.lonely_pairs
@@ -232,6 +238,16 @@
'sequence length' (default: 0.0 = no effect)" />
+
+
+
+
+
+
- 10.1371/journal.pcbi.0030065
+ 10.1371/journal.pcbi.0030065
10.1261/rna.029041.111
10.1093/bioinformatics/btv185
10.1186/s12859-014-0404-0