--- a/mummer.xml	Sat Nov 27 09:55:38 2021 +0000
+++ b/mummer.xml	Sat Oct 19 20:57:05 2024 +0000
@@ -9,7 +9,7 @@
     </expand>
     <command detect_errors="exit_code">
         <![CDATA[
-        mummer 
+        mummer
             $anchoring
             -l '$min'
             $direction
@@ -87,9 +87,9 @@
                     <option value="0">No</option>
                     <option value="1">Yes</option>
                 </param>
-                <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
+                <param  type="integer" argument="-skip" value="10" label="Sparsify"
                     help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
-                <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
+                <param  type="integer" argument="-kmer" value="1" label="kmer Table"
                     help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
             </when>
             <when value="defaults" />
@@ -112,7 +112,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test  expect_num_outputs="2">
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
             <param name="options|advanced" value="defaults" />
@@ -128,7 +128,7 @@
 
     mummer
 
-    -mumreference    Compute maximal matches that are unique in the reference- sequence but not 
+    -mumreference    Compute maximal matches that are unique in the reference- sequence but not
                      necessarily in the query-sequence (default)
 
     -maxmatch        Compute all maximal matches regardless of their uniqueness
@@ -154,16 +154,16 @@
 
     mummerplot
 
-    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                    sequence end
 
-    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
-                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                    'linespoints' instead of 'lines'
 
     -c             Generate a reference coverage plot (default for .tiling)
 
-    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                    either sequence, i.e. a one-to-one mapping of reference and query subsequences
 
     --fat          Layout sequences using fattest alignment only