Mercurial > repos > lparsons > cutadapt

diff cutadapt.xml @ 36:64172f1c1202 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit f0294a3e33257aee83aa7c507d2abddccebf0239
author iuc
date Thu, 04 Jan 2024 18:44:12 +0000
parents 9845c649f41b
children 944ae523bacb
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--- a/cutadapt.xml	Sun Dec 17 18:52:25 2023 +0000
+++ b/cutadapt.xml	Thu Jan 04 18:44:12 2024 +0000
@@ -1312,6 +1312,31 @@
                 <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>
 
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