# HG changeset patch
# User rnateam
# Date 1485038308 18000
# Node ID 94b0468f0db80bae3862e1f4449a87d8db4cfc85
# Parent  a5a2d3cefce1bd6f135113341f9802f8e51793a0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

diff -r a5a2d3cefce1 -r 94b0468f0db8 locarna_multiple.xml
--- a/locarna_multiple.xml	Fri Jan 13 16:48:50 2017 -0500
+++ b/locarna_multiple.xml	Sat Jan 21 17:38:28 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)</option>
                 <option value="local_locarna">Local alignment (LocARNA)</option>
                 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
-                <option value="sparse">Global alignment (SPARSE)</option>
+                <option value="sparse">Global fast alignment (SPARSE)</option>
             </param>
             <when value="global_locarna">
                 <param name="free_endgaps" type="select" label="Free endgaps"
@@ -119,7 +124,12 @@
                        value="1" label="Number of refinement iterations"
                        help="--iterations num" />
             </when>
-            <when value="sparse" />
+            <when value="sparse">
+                <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
+                    <expand macro="common_heuristic_parameters_sparse" />
+                </section>
+            </when>
+
         </conditional>
         
         <param name="outputs" type="select" display="checkboxes" multiple="True" 
diff -r a5a2d3cefce1 -r 94b0468f0db8 macros.xml
--- a/macros.xml	Fri Jan 13 16:48:50 2017 -0500
+++ b/macros.xml	Sat Jan 21 17:38:28 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>