--- a/locarna_pairwise.xml	Mon Dec 05 14:29:12 2022 +0000
+++ b/locarna_pairwise.xml	Mon Aug 19 18:52:50 2024 +0000
@@ -2,17 +2,12 @@
     <description>
         Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
     </description>
-
     <macros>
         <import>macros.xml</import>
     </macros>
-    
     <expand macro="requirements" />
-
     <expand macro="stdio" />
-    
     <expand macro="version" />
-   
     <command><![CDATA[
     #if str($alignment_mode.alignment_mode_selector) == "sparse"
         sparse
@@ -25,7 +20,7 @@
     
     ## --width 60
     
-    ## -------------------- alignment mode and specific options
+    ## -------------------- alignment mode and specific options ----------------#
 
     #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
         #if str($alignment_mode.free_endgaps) != "----"
@@ -54,7 +49,7 @@
 
     @CONSTRAINT_ARGS@
     
-    ## -------------------- output
+    ## -------------------- output ----------------#
     
     #if 'stockholm' in str($outputs).split(",")
         --stockholm '$stockholm'
@@ -83,32 +78,18 @@
     ]]></command>
 
     <inputs>
-        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
-               help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
-               />
-        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
-               help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
-               />
+        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
+        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
         <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)."
-                   >
-                <option value="global_locarna">Global alignment
-                (LocARNA)</option>
+            <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="sparse">Global fast alignment (SPARSE)</option>
-                <option value="structure_sequence_local_locarna">
-                    Structure and sequence local alignment (LocARNA)
-                </option>
-                <option value="structure_local_locarna">
-                    Structure local, sequence global alignment (LocARNA)
-                </option>
+                <option value="structure_sequence_local_locarna">Structure and sequence local alignment (LocARNA)</option>
+                <option value="structure_local_locarna">Structure local, sequence global alignment (LocARNA)</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="----">None</option>
                     <option value="++++">All</option>
                     <option value="+-+-">5' ends</option>
@@ -127,28 +108,21 @@
                 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE">
                     <expand macro="common_heuristic_parameters_sparse" />
                 </section>
-
              </when>
 
             <when value="structure_sequence_local_locarna" />
             <when value="structure_local_locarna" />
         </conditional>
         
-        <param name="outputs" type="select" display="checkboxes" multiple="true" 
-               label="Output options">
-            <option value="clustal_strict" selected="true">Output alignment
-            in ClustalW format</option>
-            <option value="clustal" selected="false">Output alignment
-            in constraint-annotated ClustalW format</option>
-            <option value="stockholm" selected="false">Output
-            alignment in Stockholm format</option>
-            <option value="pp" selected="false">Output
-            alignment in LocARNA's PP 2.0 format</option>
+        <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
+            <option value="clustal_strict" selected="true">Output alignment in ClustalW format</option>
+            <option value="clustal" selected="false">Output alignment in constraint-annotated ClustalW format</option>
+            <option value="stockholm" selected="false">Output alignment in Stockholm format</option>
+            <option value="pp" selected="false">Output alignment in LocARNA's PP 2.0 format</option>
         </param>
         
         <param name="stdout_verbosity" type="select" label="Standard output verbosity">
-            <option value="--quiet">Don't report standard
-            output</option>
+            <option value="--quiet">Don't report standard output</option>
             <option value="">Non verbose</option>
             <option value="--verbose">Verbose</option>
         </param>
@@ -160,9 +134,7 @@
         <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"
-                   >
+            <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>
@@ -181,20 +153,16 @@
     
     <outputs>
         <expand macro="standard_outupt" />
-        <data format="clustal" name="clustal"
-              label="${tool.name} on ${on_string}: alignment (annotated clustal)">
+        <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: alignment (annotated clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
-        <data format="clustal" name="clustal_strict" 
-              label="${tool.name}on ${on_string}: alignment (clustal)">
+        <data format="clustal" name="clustal_strict" label="${tool.name}on ${on_string}: alignment (clustal)">
             <filter>'clustal_strict' in outputs</filter>
         </data>
-        <data format="stockholm" name="stockholm"
-              label="${tool.name} on ${on_string}: alignment (stockholm)">
+        <data format="stockholm" name="stockholm" label="${tool.name} on ${on_string}: alignment (stockholm)">
             <filter>'stockholm' in outputs</filter>
         </data>
-        <data format="txt" name="pp"
-              label="${tool.name} on ${on_string}: alignment (PP 2.0)">
+        <data format="txt" name="pp" label="${tool.name} on ${on_string}: alignment (PP 2.0)">
             <filter>'pp' in outputs</filter>
         </data>
     </outputs>