--- a/locarna_multiple.xml	Mon Dec 05 14:28:49 2022 +0000
+++ b/locarna_multiple.xml	Mon Aug 19 18:52:41 2024 +0000
@@ -2,20 +2,14 @@
     <description>
         Multiple Alignment and Folding of RNAs (mlocarna)
     </description>
-
     <macros>
         <import>macros.xml</import>
     </macros>
-    
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-    
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version" />
-    
     <command><![CDATA[
     mlocarna
-    
     '$input_data'
     #if 'stockholm' in str($outputs).split(","):
     --stockholm
@@ -25,8 +19,7 @@
     ## maybe reenable later? see  https://github.com/s-will/LocARNA/issues/77
     ## --width 60
     
-    ## -------------------- alignment mode and specific options
-    #
+    ## -------------------- alignment mode and specific option--------- #
     #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
         $alignment_mode.free_endgaps
     #elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
@@ -78,30 +71,21 @@
                 <option value="text">Fasta-like input with LocARNA constraints</option>
               </param>
             <when value="fasta">
-                <param name="input_data" type="data" format="fasta" label="Sequence input"
-                       help="Sequence input in pure fasta format"
-                       />
+                <param name="input_data" type="data" format="fasta" label="Sequence input" help="Sequence input in pure fasta format"/>
             </when>
             <when value="text">
-                <param name="input_data" type="data" format="text" label="Sequence input"
-                       help="Sequence input in fasta format with locarna-specific extensions"
-                       />
+                <param name="input_data" type="data" format="text" label="Sequence input" help="Sequence input in fasta format with locarna-specific extensions"/>
             </when>
         </conditional>
         <conditional name="alignment_mode">
-            <param name="alignment_mode_selector" type="select" label="Alignment mode"
-                   help="Note that local alignment mode usually requires to turn off 
-                         the 'max-diff' heuristic (maximal difference for alignment traces)."
-                   >
+            <param name="alignment_mode_selector" type="select" label="Alignment mode" help="Note that local alignment mode usually requires to turn off the 'max-diff' heuristic (maximal difference for alignment traces).">
                 <option value="global_locarna">Global alignment (LocARNA)</option>
                 <option value="local_locarna">Local alignment (LocARNA)</option>
                 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
                 <option value="sparse">Global fast alignment (SPARSE)</option>
             </param>
             <when value="global_locarna">
-                <param name="free_endgaps" type="select" label="Free endgaps"
-                       help="Specify whether gaps at the ends (all, 5', or 3' ends)
-                             of the sequences should be penalized or allowed for free.">
+                <param name="free_endgaps" type="select" label="Free endgaps" help="Specify whether gaps at the ends (all, 5', or 3' ends)of the sequences should be penalized or allowed for free.">
                     <option value="">No free endgaps</option>
                     <option value="--free-endgaps">Free endgaps</option>
                     <option value="--free-endgaps-5">Free endgaps, only 5'</option>
@@ -111,17 +95,9 @@
             <when value="local_locarna">
             </when>
             <when value="probabilistic">
-                <param name="consistency_transformation" type="boolean" 
-                       truevalue="--consistency-transformation" falsevalue="" 
-                       checked="true" label="Consistency transformation" 
-                       help="--consistency-transformation" />
-                <param name="iterate" type="boolean"
-                       truevalue="true" falsevalue="false"
-                       checked="false" label="Iterative refinement"
-                       help="--iterate" />
-                <param name="iterations" type="integer"
-                       value="1" label="Number of refinement iterations"
-                       help="--iterations num" />
+                <param name="consistency_transformation" type="boolean" truevalue="--consistency-transformation" falsevalue="" checked="true" label="Consistency transformation" help="--consistency-transformation"/>
+                <param name="iterate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Iterative refinement" help="--iterate"/>
+                <param name="iterations" type="integer" value="1" label="Number of refinement iterations" help="--iterations num"/>
             </when>
             <when value="sparse">
                 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">