Mercurial > repos > galaxy-australia > dorado_trimming
diff dorado_trimming.xml @ 1:7ff7680fa713 draft default tip
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 42ce963fae778982b4aab4ef3b1e88480dea5053
| author | galaxy-australia |
|---|---|
| date | Mon, 11 Nov 2024 03:05:14 +0000 |
| parents | 1957f881bdf4 |
| children |
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--- a/dorado_trimming.xml Mon Nov 04 03:27:55 2024 +0000 +++ b/dorado_trimming.xml Mon Nov 11 03:05:14 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="dorado_trimming" name="Dorado adapter and primer trimming" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1"> +<tool id="dorado_trimming" name="Dorado adapter and primer trimming" version="@VERSION@+galaxy1" python_template_version="3.5" profile="24.1"> <description>for Oxford Nanopore (ONT) DNA reads</description> <macros> <import>macros.xml</import> @@ -14,11 +14,10 @@ dorado trim --verbose --threads "\${GALAXY_SLOTS}" -#if $no_trim_primers +#if $trim_primers.no_trim_primers == 'dont_trim' --no-trim-primers -#end if -#if $primer_sequences - --primer-sequences '$primer_sequences' +#else if $trim_primers.primer_sequences + --primer-sequences '${trim_primers.primer_sequences}' #end if reads > trimmed.bam @@ -33,8 +32,16 @@ ]]></command> <inputs> <param name="reads" type="data" format="bam,fastqsanger,unsorted.bam" label="Existing, basecalled DNA dataset" help="Note: this tool does not support trimming adaptors from RNA reads. These need to be removed during basecalling."/> - <param argument="--no-trim-primers" type="boolean" label="Don't trim primers" help="This option can be used to prevent the trimming of primer sequences. In this case only adapter sequences will be trimmed."/> - <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. The record names of the sequences do not matter. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/> + <conditional name="trim_primers"> + <param argument="--no-trim-primers" type="select" label="Enable primer trimming" help="Selecting 'No' prevents the trimming of primer sequences. In this case only adapter sequences will be trimmed."> + <option value="trim" selected="true">Yes</option> + <option value="dont_trim">No</option> + </param> + <when value="trim"> + <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. The record names of the sequences do not matter. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/> + </when> + <when value="dont_trim"/> + </conditional> </inputs> <outputs> <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} trimmed by the ${tool.name} tool" from_work_dir="trimmed.bam"/> @@ -43,20 +50,44 @@ <tests> <test expect_num_outputs="2"> <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/> - <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test1.bam"/> - <output name="out_tsv" ftype="tsv" file="dorado_trimming_test1.tsv"/> + <output name="out_bam" ftype="unsorted.bam"> + <assert_contents> + <has_size size="60725" delta="6000"/> + </assert_contents> + </output> + <output name="out_tsv" ftype="tsv"> + <assert_contents> + <has_text text="002f231b-5d37-437f-a027-a2e8b872e73b"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/> - <param name="no_trim_primers" value="True"/> - <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test2.bam"/> - <output name="out_tsv" ftype="tsv" file="dorado_trimming_test2.tsv"/> + <param name="no_trim_primers" value="dont_trim"/> + <output name="out_bam" ftype="unsorted.bam"> + <assert_contents> + <has_size size="60628" delta="6000"/> + </assert_contents> + </output> + <output name="out_tsv" ftype="tsv"> + <assert_contents> + <has_text text="00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <param name="reads" value="lsk109_single_read.fastqsanger.gz" ftype="fastqsanger.gz"/> <param name="primer_sequences" value="custom_primers.fasta.gz" ftype="fasta.gz"/> - <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test3.bam"/> - <output name="out_tsv" ftype="tsv" file="dorado_trimming_test3.tsv"/> + <output name="out_bam" ftype="unsorted.bam"> + <assert_contents> + <has_size size="798" delta="100"/> + </assert_contents> + </output> + <output name="out_tsv" ftype="tsv"> + <assert_contents> + <has_text text="2f707b6e-0060-4f33-9c92-a1230d26cb21"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ @@ -75,8 +106,9 @@ of the barcodes being removed, which could interfere with correct demultiplexing. -The **Don't trim primers** option can be used to prevent the trimming of -primer sequences. In this case only adapter sequences will be trimmed. +The **Enable primer trimming** option can be set to 'No' to prevent the +trimming of primer sequences. If you select 'No', only adapter sequences will +be trimmed. The output of will always be unaligned records, regardless of whether the input is aligned/sorted or not.