add missing parameters to command

or remove non existent parameters from inputs

xref bgruening#1185

tools/rna_tools/locarna/locarna_exparnap.xml

@@ -28,11 +28,13 @@
     --struct-mismatch-score $Scoring.struct_mismatch_score
 
     @HEURISTIC_ARGS@
+    --max-uil-length-ratio $Heuristics.max_uil_length_ratio
+    --max-bpil-length-ratio $Heuristics.max_bpil_length_ratio
     --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
     --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
 
     @CONSTRAINT_ARGS@
-
+    @FOLDING_ARGS@
     ## -------------------- other parameters
     #
     #if str($Other.subopt.subopt_selector) == "on"

tools/rna_tools/locarna/locarna_pairwise_p.xml

@@ -15,12 +15,12 @@
 
     <command><![CDATA[
     locarna_p
-    
+
     '$inputA'
     '$inputB'
-    
+
     @SCORING_ARGS@
-    
+
     @FOLDING_ARGS@
 
     @HEURISTIC_ARGS@
@@ -105,14 +105,6 @@
 
         <section name="Folding" title="RNA folding parameters">
             <expand macro="common_folding_parameters" />
-            <expand macro="alifold_consensus_parameter" />
-            <param name="consensus_structure" type="select" label="Consensus structure type"
-                   help="Type of consensus structures written to screen and stockholm output"
-                   >
-                <!-- <option value="mea">mea</option>-->
-                <option value="none">none</option>
-                <option value="alifold">alifold</option>
-            </param>
         </section>
 
         <section name="Heuristics" title="Heuristic parameters">