# 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