Check if cutadapt detects mispaired reads (#5696)

For issue #5655

tools/cutadapt/cutadapt.xml

@@ -1312,6 +1312,31 @@ $read_mod_options.zero_cap
                 <has_text text="-a 'GGGGGGG'"/>
             </assert_command>
         </test>
+        <!-- 44. Test mispaired read detection -->
+        <test expect_failure="true">
+            <param name="type" value="paired" />
+            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
+            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq_mispaired2.fq.gz" />
+            <section name="r1">
+                <repeat name="adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="r2">
+                <repeat name="adapters2">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="AGATCGGAAGAGC"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <assert_stdout>
+                <has_text text="Reads are improperly paired"/>
+            </assert_stdout>
+        </test>
     </tests>
 
     <help><![CDATA[

tools/cutadapt/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">4.6</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
     <xml name="edam_ontology">
         <edam_topics>