diff locarna_multiple.xml @ 2:94b0468f0db8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

--- 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"