--- a/locarna_pairwise.xml	Sat Jan 21 17:38:54 2017 -0500
+++ b/locarna_pairwise.xml	Mon Dec 05 14:29:12 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.1">
+<tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
     </description>
@@ -23,7 +23,7 @@
     '$inputA'
     '$inputB'
     
-    --width 60
+    ## --width 60
     
     ## -------------------- alignment mode and specific options
 
@@ -134,15 +134,15 @@
             <when value="structure_local_locarna" />
         </conditional>
         
-        <param name="outputs" type="select" display="checkboxes" multiple="True" 
+        <param name="outputs" type="select" display="checkboxes" multiple="true" 
                label="Output options">
-            <option value="clustal_strict" selected="True">Output alignment
+            <option value="clustal_strict" selected="true">Output alignment
             in ClustalW format</option>
-            <option value="clustal" selected="False">Output alignment
+            <option value="clustal" selected="false">Output alignment
             in constraint-annotated ClustalW format</option>
-            <option value="stockholm" selected="False">Output
+            <option value="stockholm" selected="false">Output
             alignment in Stockholm format</option>
-            <option value="pp" selected="False">Output
+            <option value="pp" selected="false">Output
             alignment in LocARNA's PP 2.0 format</option>
         </param>
         
@@ -182,36 +182,36 @@
     <outputs>
         <expand macro="standard_outupt" />
         <data format="clustal" name="clustal"
-              label="${tool.name} alignment (annotated clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (annotated clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="clustal" name="clustal_strict" 
-              label="${tool.name} alignment (clustal) on ${on_string}">
+              label="${tool.name}on ${on_string}: alignment (clustal)">
             <filter>'clustal_strict' in outputs</filter>
         </data>
         <data format="stockholm" name="stockholm"
-              label="${tool.name} alignment (stockholm) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (stockholm)">
             <filter>'stockholm' in outputs</filter>
         </data>
         <data format="txt" name="pp"
-              label="${tool.name} alignment (PP 2.0) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (PP 2.0)">
             <filter>'pp' in outputs</filter>
         </data>
     </outputs>
     
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="clustal" />
             <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputA" value="haca.snoRNA-1.aln" />
             <param name="inputB" value="haca.snoRNA-2.aln" />
             <param name="outputs" value="clustal_strict,clustal" />
             <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
-            <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="1" />
+            <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="2" />
         </test>
     </tests>