not finished to fix all remarks

tools/shovill/shovill.xml

@@ -135,7 +135,7 @@
         </data>
     </outputs>
     <tests>
-        <test> <!-- Test 1: Basic test -->
+        <test expect_num_outputs="3"> <!-- Test 1: Basic test -->
             <param name="lib_type" value="paired" />
             <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
             <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
@@ -153,7 +153,7 @@
                   </assert_contents>
                 </output>
         </test>
-        <test> <!-- Test 2: Auto everything + trim + different name format test -->
+        <test expect_num_outputs="3"> <!-- Test 2: Auto everything + trim + different name format test -->
             <param name="lib_type" value="paired" />
             <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
             <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
@@ -184,7 +184,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 3: Alternate assembler #1: Megahit -->
+        <test expect_num_outputs="3"> <!-- Test 3: Alternate assembler #1: Megahit -->
             <param name="lib_type" value="paired" />
             <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
             <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
@@ -203,7 +203,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 4: Alternate assembler #2: Skesa -->
+        <test expect_num_outputs="3"> <!-- Test 4: Alternate assembler #2: Skesa -->
             <param name="lib_type" value="paired" />
             <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
             <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
@@ -222,7 +222,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 5: Alternate assembler #3: Velvet -->
+        <test expect_num_outputs="3"> <!-- Test 5: Alternate assembler #3: Velvet -->
             <param name="lib_type" value="paired" />
             <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
             <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
@@ -241,7 +241,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test> <!-- Test 6: Gzipped input with trimming -->
+        <test expect_num_outputs="3"> <!-- Test 6: Gzipped input with trimming -->
             <param name="lib_type" value="paired" />
             <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" />
             <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" />