comparison cutadapt.xml @ 36:64172f1c1202 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit f0294a3e33257aee83aa7c507d2abddccebf0239

35:9845c649f41b

                <has_text text="--match-read-wildcards"/>
                <has_text text="--error-rate=0.0"/>
                <has_text text="-a 'GGGGGGG'"/>
            </assert_command>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark

36:64172f1c1202

                <has_text text="--match-read-wildcards"/>
                <has_text text="--error-rate=0.0"/>
                <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[

.. class:: infomark