Mercurial > repos > lparsons > cutadapt
changeset 36:64172f1c1202 draft
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 |
| files | cutadapt.xml macros.xml test-data/bwa-mem-fastq_mispaired2.fq.gz |
| diffstat | 3 files changed, 26 insertions(+), 1 deletions(-) [+] |
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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> <help><![CDATA[
--- a/macros.xml Sun Dec 17 18:52:25 2023 +0000 +++ b/macros.xml Thu Jan 04 18:44:12 2024 +0000 @@ -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>