# HG changeset patch
# User rnateam
# Date 1485037366 18000
# Node ID 10bb7c63d55197e311d6535c2511f4c24e91a00d
# Parent  a2bc02c2bebc383adde0a4de1e8bfa9dd13c5ae0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

diff -r a2bc02c2bebc -r 10bb7c63d551 macros.xml
--- a/macros.xml	Fri Jan 13 16:44:17 2017 -0500
+++ b/macros.xml	Sat Jan 21 17:22:46 2017 -0500
@@ -141,6 +141,12 @@
         #end if
     </token>
 
+    <token name="@HEURISTIC_SPARSE_ARGS@">
+           --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
+           --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
+
+    </token>
+
     <token name="@CONSTRAINT_ARGS@">
         ## -------------------- constraint parameters
         $Constraints.lonely_pairs
@@ -232,6 +238,16 @@
                        'sequence length' (default: 0.0 = no effect)" />
     </xml>
     
+    <xml name="common_heuristic_parameters_sparse">
+        <param  name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
+                min="0.0" max="0.2"
+                label="Probability threshold for unpaired bases in loops" /> 
+
+        <param  name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" 
+                min="0.0" max="0.2"
+                label="Probability threshold for base pairs in loops" />       
+    </xml>
+    
     <xml name="in_loop_ratio_parameters">
         <param  name="max_uil_length_ratio" argument="max-uil-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
@@ -308,8 +324,7 @@
 
     <xml name="citations">
         <citations>
-            <citation
-            type="doi">10.1371/journal.pcbi.0030065</citation>
+            <citation type="doi">10.1371/journal.pcbi.0030065</citation>
             <citation type="doi">10.1261/rna.029041.111</citation>
             <citation type="doi">10.1093/bioinformatics/btv185</citation>
             <citation type="doi">10.1186/s12859-014-0404-0</citation>