# HG changeset patch
# User rnateam
# Date 1485037343 18000
# Node ID f8c5261fafdc545c3a91062aa1692a32c3e4177a
# Parent 3a4167720464858494b236a3e8816bb8100c4f97
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
diff -r 3a4167720464 -r f8c5261fafdc locarna_multiple.xml
--- a/locarna_multiple.xml Fri Jan 13 16:43:47 2017 -0500
+++ b/locarna_multiple.xml Sat Jan 21 17:22:23 2017 -0500
@@ -52,6 +52,11 @@
$Folding.alifold_consensus_dp
@HEURISTIC_ARGS@
+
+ #if str($alignment_mode.alignment_mode_selector) == "sparse"
+ --pw-aligner-options " @HEURISTIC_SPARSE_ARGS@ "
+ #end if
+
@CONSTRAINT_ARGS@
#if str($Constraints.bed_anchors.bed_anchors_selector) == "yes"
@@ -92,7 +97,7 @@
(LocARNA)
-
+
-
+
+
+
+
+
+ --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