comparison cutadapt.xml @ 40:aa784cb3810d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 8bdd212b8708a9d080e87303dd543fb93bc05c2f

39:fe74900d6dc7

#if str($other_trimming_options.shorten_options.shorten_values) == 'True':
    #if str($other_trimming_options.shorten_options.shorten_end) == '3prime'
        --length=$other_trimming_options.shorten_options.length
    #else
        --length=-$other_trimming_options.shorten_options.length
    #end if
#end if

$filter_options.discard_trimmed
$filter_options.discard_untrimmed

            <param name="action" type="select" label="What to do if a match is found">
                <option value="trim" selected="true">Trim: trim adapter and upstream or downstream sequence</option>
                <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
                <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
                <option value="lowercase">Lowercase: convert to lowercase</option>
                <option value="none">None: leave unchanged</option>
            </param>
            <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
            <param argument="--no-indels" type="boolean" checked="false" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
            <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />

                    <option value="False" selected="true">Disabled</option>
                </param>
                <when value="True">
                    <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
                    <param name="shorten_end" type="select" label="End at which to apply the slice">
                        <option value="3prime">3' ends</option>
                        <option value="5prime">5' ends</option>
                    </param>
                </when>
                <when value="False">

                        <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 -->

            <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">

                        <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"/>
                <param name="maximum_length2" value="30"/>

            <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"/>

            </section>
            <section name="filter_options">
                <param name="minimum_length" value="0"/>
            </section>
            <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
        </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" />

40:aa784cb3810d

#if str($other_trimming_options.shorten_options.shorten_values) == 'True':
    #if str($other_trimming_options.shorten_options.shorten_end) == '3prime'
        --length=$other_trimming_options.shorten_options.length
    #else
        --length=-$other_trimming_options.shorten_options.length
    #end if
#end if
#if $paired and str($other_trimming_options.shorten_options_r2.shorten_values_r2) == 'True':
    #if str($other_trimming_options.shorten_options_r2.shorten_end_r2) == '3prime'
        -L $other_trimming_options.shorten_options_r2.length2
    #else
        -L -$other_trimming_options.shorten_options_r2.length2
    #end if
#end if

$filter_options.discard_trimmed
$filter_options.discard_untrimmed

            <param name="action" type="select" label="What to do if a match is found">
                <option value="trim" selected="true">Trim: trim adapter and upstream or downstream sequence</option>
                <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
                <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
                <option value="lowercase">Lowercase: convert to lowercase</option>
                <option value="crop">Crop: trim upstream and downstream sequences, i.e. retain adapter sequences only</option>
                <option value="none">None: leave unchanged</option>
            </param>
            <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
            <param argument="--no-indels" type="boolean" checked="false" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
            <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />

                    <option value="False" selected="true">Disabled</option>
                </param>
                <when value="True">
                    <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
                    <param name="shorten_end" type="select" label="End at which to apply the slice">
                        <option value="3prime">3' ends</option>
                        <option value="5prime">5' ends</option>
                    </param>
                </when>
                <when value="False">
                </when>
            </conditional>
            <conditional name="shorten_options_r2">
                <param name="shorten_values_r2" type="select" label="Separate shortening of R2 reads to a fixed length?" help="For paired-end data, shortening of R2 reads can be handled separately. Ignored for single-end data.">
                    <option value="True">Separate shortening of R2 reads</option>
                    <option value="False" selected="true">Treat R2 reads the same as R1 reads</option>
                </param>
                <when value="True">
                    <param argument="-L" name="length2" type="integer" value="0" label="Length" help="Shorten R2 reads to this length. This modification is applied after adapter trimming." />
                    <param name="shorten_end_r2" type="select" label="End at which to apply the slice">
                        <option value="3prime">3' ends</option>
                        <option value="5prime">5' ends</option>
                    </param>
                </when>
                <when value="False">

                        <param name="adapter" value="CGTCCGAANTAG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="adapter_options">
                <param name="action" value="crop"/>
            </section>
            <output name="out1" file="cutadapt_action_crop.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 -->

            <section name="adapter_options">
                <param name="revcomp" value="true"/>
            </section>
            <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
        </test>
        <!-- Test 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">

                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" 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"/>
                <param name="maximum_length2" value="30"/>

            <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="filter_options">
                <param name="pair_filter" value="both"/>

            </section>
            <section name="filter_options">
                <param name="minimum_length" value="0"/>
            </section>
            <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <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="r2">
                <repeat name="adapters2">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGCCGCTANGACG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="other_trimming_options">
                <conditional name="shorten_options">
                    <param name="shorten_values" value="True"/>
                    <param name="shorten_end" value="3prime"/>
                    <param name="length" value="10"/>
                </conditional>
                <conditional name="shorten_options_r2">
                    <param name="shorten_values_r2" value="True"/>
                    <param name="shorten_end_r2" value="5prime"/>
                    <param name="length2" value="10"/>
                </conditional>
            </section>
            <section name="filter_options">
                <param name="minimum_length" value="0"/>
            </section>
            <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
            <output name="out2" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
        </test>
        <test expect_num_outputs="2">
            <param name="type" value="paired" />
            <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
            <section name="r2">
                <repeat name="adapters2">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGCCGCTANGACG"/>
                    </conditional>
                </repeat>
            </section>
            <section name="other_trimming_options">
                <conditional name="shorten_options_r2">
                    <param name="shorten_values_r2" value="True"/>
                    <param name="shorten_end_r2" value="3prime"/>
                    <param name="length2" value="10"/>
                </conditional>
            </section>
            <section name="filter_options">
                <param name="minimum_length" value="0"/>
            </section>
            <output name="out1" file="cutadapt_small.fastq" ftype="fastq"/>
            <output name="out2" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
        </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" />