comparison cutadapt.xml @ 25:4e5056fefd88 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"

24:288f97432497

        --length=-$read_mod_options.shorten_options.length
    #end if
#end if
#if str($read_mod_options.length_tag) != '':
    --length-tag='$read_mod_options.length_tag'
#end if
#if str($read_mod_options.cut) != '0':
    --cut=$read_mod_options.cut
#end if
#if str($read_mod_options.rename) != '':
    --rename='$read_mod_options.rename'
#end if
$read_mod_options.zero_cap

                    <param name="R2_minimum" type="integer" min="0" value="" optional="True" label="Minimum length (R2)" />
                    <param name="R2_maximum" type="integer" min="0" value="" optional="True" label="Maximum length (R2)" />
                </when>
                <when value="False">
                </when>
            </conditional>   
            <param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
            <param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
                <option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
                <option value="both">Both: filtering criteria must apply to both reads in order for a read pair to be discarded. </option>
                <option value="first">First: will make a decision about the read pair by inspecting whether the filtering criterion applies to the first read, ignoring the second read.</option>

                        <add value=" " />
                    </valid>
                </sanitizer>
                <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
            </param>
            <param argument="--cut" label="Remove a fixed number of bases" type="integer" value="0" help="This option allows to unconditionally remove bases from the beginning or end of each read. If the given length is positive, the bases are removed from the beginning of each read. If it is negative, the bases are removed from the end." />
            <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
        </section>

        <!-- Output Options -->
        <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Outputs selector">

    <tests>
        <!-- Ensure fastq works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
        </test>
        <!-- Ensure single end fastq.gz works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
        </test>
        <!-- Ensure paired end fastq.gz works -->
        <test expect_num_outputs="2">
            <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-fastq2.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
            <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
            <assert_command>
                <not_has_text text="--discard-trimmed"/>
                <not_has_text text="--discard-untrimmed"/>

                <collection type="paired">
                    <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
                    <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
                </collection>
            </param>
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <output_collection name="out_pairs" type="paired">
                <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
                <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
            </output_collection>
        </test>
        <!-- Ensure built-in adapters work -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="builtin"/>
            <param name="adapter" value="TGTAGGCC"/>
            <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
        </test>
        <!-- Ensure discard file output works -->
        <test expect_num_outputs="1">
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="TTAGACATATCTCCGTCG"/>
            <param name="output_filtering" value="filter"/>
            <section name="filter_options">
                <param name="discard_trimmed" value="True"/>
            </section>
            <param name="read_modification" value="none"/>

            </assert_command>
        </test>
        <!-- Ensure rest file output works -->
        <test expect_num_outputs="2">
            <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AAAGATG"/>
            <param name="output_filtering" value="default"/>
            <param name="read_modification" value="none"/>
            <param name="output_selector" value="rest_file"/>
            <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
            <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
        </test>
        <!-- Ensure nextseq-trim option works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="read_modification" value="modify"/>
            <param name="nextseq_trim" value="20" />
            <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
        </test>
        <!-- Ensure Report and Info file output work -->
        <test expect_num_outputs="3">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="output_selector" value="report,info_file" />
            <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
            <output name="report">
                <assert_contents>
                    <has_text text="Summary"/>

        <!-- Ensure untrimmed file output works -->
        <test expect_num_outputs="2">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AAAT"/>
            <param name="output_selector" value="untrimmed_file" />
            <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
            <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
        </test>
        <!-- Ensure untrimmed gzip file output works -->
        <test expect_num_outputs="2">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="output_selector" value="untrimmed_file" />
            <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
            <!-- 
                Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
                See discussion at https://github.com/galaxyproject/galaxy/issues/7671
                `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
                difference between level 1 compression and no compression
            -->

        <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->
        <test expect_num_outputs="2">
            <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-fastq2.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="filter_options">
                <param name="discard_untrimmed" value="true"/>
                <param name="minimun_length" value="1"/>
                <param name="maximum_length" value="1000"/>
                <param name="max_n" value="0"/>

        </test>
        <!-- Test cut option -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
             <section name="read_mod_options">
                <param name="cut" value="5"/>
            </section>
            <output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
        </test>
        <!-- Test rename options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <section name="read_mod_options">
                <param name="cut" value="5"/>
                <param name="rename" value="{id} barcode={cut_prefix}"/>
            </section>
            <output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
                <assert_contents>
                    <has_text text="@prefix:1_13_1259/1 barcode=AGCCG"/>

        </test>
        <!-- Test action options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="CGTCCGAANTAG"/>
            <section name="adapter_options">
                <param name="action" value="retain"/>
            </section>
            <output name="out1" file="cutadapt_action_retain.out" ftype="fastq"/>
        </test>
           <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="CGTCCGAANTAG"/>
            <section name="adapter_options">
                <param name="action" value="mask"/>
            </section>
            <output name="out1" file="cutadapt_action_mask.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="CGTCCGAANTAG"/>
            <section name="adapter_options">
                <param name="action" value="lowercase"/>
            </section>
            <output name="out1" file="cutadapt_action_lowercase.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="CGTCCGAANTAG"/>
            <section name="adapter_options">
                <param name="action" value="none"/>
            </section>
            <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
        </test>
        <!-- Test revcomp options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="TAAACAGATTAGT"/>
            <section name="adapter_options">
                <param name="revcomp" value="true"/>
            </section>
            <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
        </test>
        <!-- Test minimum lenghth paired-reads -->
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="ATCTGGTTCC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="CTACAAG"/>
            <section name="filter_options">
                <param name="minimum_length" value="30"/>
                <param name="pair_filter" value="both"/>
                <conditional name="length_R2_options">
                    <param name="length_R2_status" value="True"/>

        <!-- Test maximum lenghth paired-reads -->
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="filter_options">
                <param name="pair_filter" value="both"/>
                <param name="maximum_length" value="50"/>
                <conditional name="length_R2_options">
                    <param name="length_R2_status" value="True"/>

        <!-- Test combination maximum and minimum length paired reads -->
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="filter_options">
                <param name="pair_filter" value="both"/>
                <param name="minimum_length" value="10"/>
                <param name="maximum_length" value="50"/>
                <conditional name="length_R2_options">

        </test>
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="filter_options">
                <param name="pair_filter" value="both"/>
                <param name="minimum_length" value="10"/>
                <param name="maximum_length" value="50"/>
                <conditional name="length_R2_options">

        </test>
        <!-- Test length options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGCCGCTANGACG"/>
            <section name="read_mod_options">
                <conditional name="shorten_options">
                    <param name="shorten_values" value="True"/>
                    <param name="shorten_end" value="3prime"/>
                    <param name="length" value="10"/>

            <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGCCGCTANGACG"/>
            <section name="read_mod_options">
                <conditional name="shorten_options">
                    <param name="shorten_values" value="True"/>
                    <param name="shorten_end" value="5prime"/>
                    <param name="length" value="10"/>

        </test>
        <!-- Test max expected errors options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGCGGCTTAGACG"/>
            <section name="filter_options">
                <param name="max_expected_errors" value="10"/>
            </section>
            <output name="out1" file="cutadapt_shorten_expected_errors.out" ftype="fastq"/>
        </test>
        <!-- Test disallow internal adaptors option -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="GAANTAGCTACCAC"/>
            <section name="adapter_options">
                <param name="internal" value="X"/>
            </section>
            <output name="out1" file="cutadapt_shorten_internal_adapters.out" ftype="fastq"/>
            <assert_command>

        </test>
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
            <param name="adapter_source_list" value="user"/>
            <param name="adapter" value="AGATCGGAAGAGC"/>
            <param name="adapter_source_list2" value="user"/>
            <param name="adapter2" value="AGATCGGAAGAGC"/>
            <section name="adapter_options">
                <param name="internal" value="X"/>
            </section>
            <output name="out1" decompress="True" file="cutadapt_out1_internal_adapter.fq.gz" ftype="fastq.gz"/>
            <output name="out2" decompress="True" file="cutadapt_out2_internal_adapter.fq.gz" ftype="fastq.gz"/>

            </assert_command>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <param name="adapter_source_list" value="builtin"/>
            <param name="adapter" value="TGTAGGCC"/>
            <section name="adapter_options">
                <param name="internal" value="X"/>
            </section>
            <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
            <assert_command>

25:4e5056fefd88

        --length=-$read_mod_options.shorten_options.length
    #end if
#end if
#if str($read_mod_options.length_tag) != '':
    --length-tag='$read_mod_options.length_tag'
#end if
#if str($read_mod_options.rename) != '':
    --rename='$read_mod_options.rename'
#end if
$read_mod_options.zero_cap

                    <param name="R2_minimum" type="integer" min="0" value="" optional="True" label="Minimum length (R2)" />
                    <param name="R2_maximum" type="integer" min="0" value="" optional="True" label="Maximum length (R2)" />
                </when>
                <when value="False">
                </when>
            </conditional>
            <param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
            <param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
                <option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
                <option value="both">Both: filtering criteria must apply to both reads in order for a read pair to be discarded. </option>
                <option value="first">First: will make a decision about the read pair by inspecting whether the filtering criterion applies to the first read, ignoring the second read.</option>

                        <add value=" " />
                    </valid>
                </sanitizer>
                <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
            </param>
            <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
        </section>

        <!-- Output Options -->
        <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Outputs selector">

    <tests>
        <!-- Ensure fastq works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <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>
            <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
        </test>
        <!-- Ensure single end fastq.gz works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.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>
            <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
        </test>
        <!-- Ensure paired end fastq.gz works -->
        <test expect_num_outputs="2">
            <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-fastq2.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_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
            <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
            <assert_command>
                <not_has_text text="--discard-trimmed"/>
                <not_has_text text="--discard-untrimmed"/>

                <collection type="paired">
                    <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
                    <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
                </collection>
            </param>
            <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_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <output_collection name="out_pairs" type="paired">
                <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
                <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
            </output_collection>
        </test>
        <!-- Ensure built-in adapters work -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="builtin"/>
                        <param name="adapter" value="TGTAGGCC"/>
                    </conditional>
                </repeat>
            </section>
            <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
        </test>
        <!-- Ensure discard file output works -->
        <test expect_num_outputs="1">
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="TTAGACATATCTCCGTCG"/>
                    </conditional>
                </repeat>
            </section>
            <param name="output_filtering" value="filter"/>
            <section name="filter_options">
                <param name="discard_trimmed" value="True"/>
            </section>
            <param name="read_modification" value="none"/>

            </assert_command>
        </test>
        <!-- Ensure rest file output works -->
        <test expect_num_outputs="2">
            <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AAAGATG"/>
                    </conditional>
                </repeat>
            </section>
            <param name="output_filtering" value="default"/>
            <param name="read_modification" value="none"/>
            <param name="output_selector" value="rest_file"/>
            <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
            <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
        </test>
        <!-- Ensure nextseq-trim option works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.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>
            <param name="read_modification" value="modify"/>
            <param name="nextseq_trim" value="20" />
            <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
        </test>
        <!-- Ensure Report and Info file output work -->
        <test expect_num_outputs="3">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <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>
            <param name="output_selector" value="report,info_file" />
            <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
            <output name="report">
                <assert_contents>
                    <has_text text="Summary"/>

        <!-- Ensure untrimmed file output works -->
        <test expect_num_outputs="2">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AAAT"/>
                    </conditional>
                </repeat>
            </section>
            <param name="output_selector" value="untrimmed_file" />
            <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
            <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
        </test>
        <!-- Ensure untrimmed gzip file output works -->
        <test expect_num_outputs="2">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.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>
            <param name="output_selector" value="untrimmed_file" />
            <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
            <!--
                Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
                See discussion at https://github.com/galaxyproject/galaxy/issues/7671
                `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
                difference between level 1 compression and no compression
            -->

        <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->
        <test expect_num_outputs="2">
            <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-fastq2.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="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="filter_options">
                <param name="discard_untrimmed" value="true"/>
                <param name="minimun_length" value="1"/>
                <param name="maximum_length" value="1000"/>
                <param name="max_n" value="0"/>

        </test>
        <!-- Test cut option -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
                <param name="cut" value="5"/>
            </section>
            <output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
        </test>
        <!-- Test rename options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
                <param name="cut" value="5"/>
            </section>
            <section name="read_mod_options">
                <param name="rename" value="{id} barcode={cut_prefix}"/>
            </section>
            <output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
                <assert_contents>
                    <has_text text="@prefix:1_13_1259/1 barcode=AGCCG"/>

        </test>
        <!-- Test action options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="CGTCCGAANTAG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="action" value="retain"/>
            </section>
            <output name="out1" file="cutadapt_action_retain.out" ftype="fastq"/>
        </test>
           <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="CGTCCGAANTAG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="action" value="mask"/>
            </section>
            <output name="out1" file="cutadapt_action_mask.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="CGTCCGAANTAG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="action" value="lowercase"/>
            </section>
            <output name="out1" file="cutadapt_action_lowercase.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="CGTCCGAANTAG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="action" value="none"/>
            </section>
            <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
        </test>
        <!-- Test revcomp options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="TAAACAGATTAGT"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="revcomp" value="true"/>
            </section>
            <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
        </test>
        <!-- Test minimum lenghth paired-reads -->
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="ATCTGGTTCC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="r2">
                <repeat name="adapters2">
                    <conditional name="adapter_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="CTACAAG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="filter_options">
                <param name="minimum_length" value="30"/>
                <param name="pair_filter" value="both"/>
                <conditional name="length_R2_options">
                    <param name="length_R2_status" value="True"/>

        <!-- Test maximum lenghth paired-reads -->
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.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_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="filter_options">
                <param name="pair_filter" value="both"/>
                <param name="maximum_length" value="50"/>
                <conditional name="length_R2_options">
                    <param name="length_R2_status" value="True"/>

        <!-- Test combination maximum and minimum length paired reads -->
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.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_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="filter_options">
                <param name="pair_filter" value="both"/>
                <param name="minimum_length" value="10"/>
                <param name="maximum_length" value="50"/>
                <conditional name="length_R2_options">

        </test>
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.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_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="filter_options">
                <param name="pair_filter" value="both"/>
                <param name="minimum_length" value="10"/>
                <param name="maximum_length" value="50"/>
                <conditional name="length_R2_options">

        </test>
        <!-- Test length options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGCCGCTANGACG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="read_mod_options">
                <conditional name="shorten_options">
                    <param name="shorten_values" value="True"/>
                    <param name="shorten_end" value="3prime"/>
                    <param name="length" value="10"/>

            <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGCCGCTANGACG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="read_mod_options">
                <conditional name="shorten_options">
                    <param name="shorten_values" value="True"/>
                    <param name="shorten_end" value="5prime"/>
                    <param name="length" value="10"/>

        </test>
        <!-- Test max expected errors options -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGCGGCTTAGACG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="filter_options">
                <param name="max_expected_errors" value="10"/>
            </section>
            <output name="out1" file="cutadapt_shorten_expected_errors.out" ftype="fastq"/>
        </test>
        <!-- Test disallow internal adaptors option -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="GAANTAGCTACCAC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="internal" value="X"/>
            </section>
            <output name="out1" file="cutadapt_shorten_internal_adapters.out" ftype="fastq"/>
            <assert_command>

        </test>
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
            <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.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_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="internal" value="X"/>
            </section>
            <output name="out1" decompress="True" file="cutadapt_out1_internal_adapter.fq.gz" ftype="fastq.gz"/>
            <output name="out2" decompress="True" file="cutadapt_out2_internal_adapter.fq.gz" ftype="fastq.gz"/>

            </assert_command>
        </test>
        <test expect_num_outputs="1">
            <param name="type" value="single" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="builtin"/>
                        <param name="adapter" value="TGTAGGCC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="internal" value="X"/>
            </section>
            <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
            <assert_command>