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Dorado basecaller
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| --- | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "{{ tool_name }} from the dorado suite" | ||
| categories: | ||
| - Sequence Analysis | ||
| description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
| exclude: | ||
| - tool_test_output.html | ||
| - tool_test_output.json | ||
| homepage_url: https://github.com/nanoporetech/dorado | ||
| long_description: > | ||
| Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
| name: dorado | ||
| owner: galaxy-australia | ||
| remote_repository_url: https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado | ||
| suite: | ||
| name: suite_dorado | ||
| description: > | ||
| Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
| long_description: > | ||
| Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
| type: unrestricted |
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| ## Tool versions | ||
|
|
||
| Dorado is distributed on | ||
| [DockerHub](https://hub.docker.com/r/nanoporetech/dorado/tags) by nanoporetech. | ||
| The containers are identified by sha256 hash, but not tagged with a version. | ||
|
|
||
| We can still use the containers and display the dorado version by hard-coding | ||
| both dorado version and container hash into the wrapper (see `macros.xml`). | ||
| Unfortunately you have to pull a >6 GB container and run `dorado --version` just | ||
| to check the tool version. This also prevents auto-updates of this wrapper. | ||
|
|
||
| You can update the list of models at the same time (see | ||
| below). **You must do this when you update the wrapper**. | ||
|
|
||
| ## Basecalling models | ||
|
|
||
| The models are bundled in the container at `/models` and made available by the | ||
| `dorado_models.loc` file. | ||
|
|
||
| The columns are `value`, `container_hash`, `name` and `path`. | ||
|
|
||
| To update the list, modify `tool-data/dorado_models.loc.sample`. | ||
|
|
||
| Because models can be added and removed, models are listed **per container** in | ||
| the loc file. | ||
|
|
||
| Here's some code to **append** the models from the container with hash | ||
| `1c65eb070a9fc1d88710c4dc09b06541f96fdd28` to the loc file. | ||
|
|
||
| ```bash | ||
| export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28" | ||
|
|
||
| apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \ | ||
| ls /models | \ | ||
| awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \ | ||
| >> tool-data/dorado_models.loc.sample | ||
| ``` | ||
|
|
||
| The loc file doesn't have a header, so you can keep it sorted. | ||
|
|
||
| ```bash | ||
| cp tool-data/dorado_models.loc.sample \ | ||
| tool-data/dorado_models.loc.sample.old && | ||
| sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample.old \ | ||
| > tool-data/dorado_models.loc | ||
| ``` | ||
|
|
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| <tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> | ||
| <description>basecaller for raw Oxford Nanopore data</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$pod5_file' ./reads.pod5 | ||
| && | ||
| dorado basecaller | ||
| --trim '${trim}' | ||
| #if $kit_name | ||
| --kit-name '${kit_name}' | ||
| #end if | ||
| '${model.fields.path}' | ||
| reads.pod5 | ||
| > calls.bam | ||
| && | ||
| dorado summary | ||
| calls.bam | ||
| > summary.tsv | ||
| ]]></command> | ||
| <inputs> | ||
| <!-- FIXME: add pod5 datatype to Galaxy and change here. | ||
| https://github.com/galaxyproject/galaxy/pull/18419 --> | ||
| <param name="pod5_file" type="data" format="binary" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/> | ||
| <param name="model" type="select" label="Basecalling model. See the Help section for info on model names."> | ||
| <options from_data_table="dorado_models"> | ||
| <!-- only allow models that shipped in this container --> | ||
| <filter type="static_value" column="1" value="@CONTAINER_HASH@"/> | ||
| </options> | ||
| </param> | ||
| <param type="select" argument="--trim" label="DNA adapter and primer trimming" help="Detect and remove any adapter and/or primer sequences from the beginning and end of DNA reads. Note that if you intend to demultiplex the reads, trimming adapters and primers could interfere with correct demultiplexing."> | ||
| <option value="all" selected="true">Any. Trim any detected adapters or primers.</option> | ||
| <option value="primers"> Primers. Trim any detected adapters or primers, but if barcoding is enabled the barcode sequences will not be trimmed.</option> | ||
| <option value="adapters"> Adapters. Trim any detected adapters, but primers will not be trimmed, and if barcoding is enabled then barcodes will not be trimmed either.</option> | ||
| <option value="none"> None. Nothing will be trimmed.</option> | ||
| </param> | ||
| <param type="select" argument="--kit-name" optional="true" label="Enable barcoding with the selected kit name." help="Reads are classified into their barcode groups during basecalling. The classification will be reflected in the read group name as well as in the BC tag of the output record."> | ||
| <option value="EXP-NBD103">EXP-NBD103</option> | ||
| <option value="EXP-NBD104">EXP-NBD104</option> | ||
| <option value="EXP-NBD114">EXP-NBD114</option> | ||
| <option value="EXP-NBD196">EXP-NBD196</option> | ||
| <option value="EXP-PBC001">EXP-PBC001</option> | ||
| <option value="EXP-PBC096">EXP-PBC096</option> | ||
| <option value="SQK-16S024">SQK-16S024</option> | ||
| <option value="SQK-16S114-24">SQK-16S114-24</option> | ||
| <option value="SQK-LWB001">SQK-LWB001</option> | ||
| <option value="SQK-MLK111-96-XL">SQK-MLK111-96-XL</option> | ||
| <option value="SQK-MLK114-96-XL">SQK-MLK114-96-XL</option> | ||
| <option value="SQK-NBD111-24">SQK-NBD111-24</option> | ||
| <option value="SQK-NBD111-96">SQK-NBD111-96</option> | ||
| <option value="SQK-NBD114-24">SQK-NBD114-24</option> | ||
| <option value="SQK-NBD114-96">SQK-NBD114-96</option> | ||
| <option value="SQK-PBK004">SQK-PBK004</option> | ||
| <option value="SQK-PCB109">SQK-PCB109</option> | ||
| <option value="SQK-PCB110">SQK-PCB110</option> | ||
| <option value="SQK-PCB111-24">SQK-PCB111-24</option> | ||
| <option value="SQK-PCB114-24">SQK-PCB114-24</option> | ||
| <option value="SQK-RAB201">SQK-RAB201</option> | ||
| <option value="SQK-RAB204">SQK-RAB204</option> | ||
| <option value="SQK-RBK001">SQK-RBK001</option> | ||
| <option value="SQK-RBK004">SQK-RBK004</option> | ||
| <option value="SQK-RBK110-96">SQK-RBK110-96</option> | ||
| <option value="SQK-RBK111-24">SQK-RBK111-24</option> | ||
| <option value="SQK-RBK111-96">SQK-RBK111-96</option> | ||
| <option value="SQK-RBK114-24">SQK-RBK114-24</option> | ||
| <option value="SQK-RBK114-96">SQK-RBK114-96</option> | ||
| <option value="SQK-RLB001">SQK-RLB001</option> | ||
| <option value="SQK-RPB004">SQK-RPB004</option> | ||
| <option value="SQK-RPB114-24">SQK-RPB114-24</option> | ||
| <option value="TWIST-16-UDI">TWIST-16-UDI</option> | ||
| <option value="TWIST-96A-UDI">TWIST-96A-UDI</option> | ||
| <option value="VSK-PTC001">VSK-PTC001</option> | ||
| <option value="VSK-VMK001">VSK-VMK001</option> | ||
| <option value="VSK-VMK004">VSK-VMK004</option> | ||
| <option value="VSK-VPS001">VSK-VPS001</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} basecalled by ${tool.name} with model ${model.fields.name}" from_work_dir="calls.bam"/> | ||
| <data format="tsv" name="out_tsv" label="${tool.name} sequencing summary for ${on_string}" from_work_dir="summary.tsv"/> | ||
| </outputs> | ||
| <tests> | ||
| <!-- test 1 --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="pod5_file" value="FAL00375_473bf0ed_0.ten_reads.pod5"/> | ||
| <param name="model" value="[email protected]"/> | ||
| <param name="trim" value="all"/> | ||
| <output name="out_bam" ftype="unsorted.bam"> | ||
| <assert_contents> | ||
| <has_size size="10000" delta="1000"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_tsv" ftype="tsv"> | ||
| <assert_contents> | ||
| <has_text text="00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- test 2: trim parameter --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="pod5_file" value="FAL00375_473bf0ed_0.ten_reads.pod5"/> | ||
| <param name="model" value="[email protected]"/> | ||
| <param name="trim" value="adapters"/> | ||
| <output name="out_bam" ftype="unsorted.bam"> | ||
| <assert_contents> | ||
| <has_size size="10000" delta="1000"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_tsv" ftype="tsv"> | ||
| <assert_contents> | ||
| <has_text text="0072b26f-f37c-4517-afa7-621543ac2187"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- test 3: barcode detection --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="pod5_file" value="SQK-RBK114_BC01_BC04_unclassified.pod5"/> | ||
| <param name="model" value="[email protected]"/> | ||
| <param name="trim" value="all"/> | ||
| <param name="kit_name" value="SQK-RBK114-96"/> | ||
| <output name="out_bam" ftype="unsorted.bam"> | ||
| <assert_contents> | ||
| <has_size size="10000" delta="1000"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_tsv" ftype="tsv"> | ||
| <assert_contents> | ||
| <has_size size="1103e241-dd7f-43bc-ae19-9a3c6326ad83"/> | ||
| <has_text text="SQK-RBK114-96_barcode04"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| Basecall raw Nanopore data using Oxford Nanopore’s open source | ||
| `dorado <https://github.com/nanoporetech/dorado/>`__ basecaller. | ||
| The input is pod5 format. If you have older data in fast5 format, you | ||
| can convert them using the ``fast5 to pod5`` convert tool. | ||
| Basecalling models | ||
| ------------------ | ||
| **TLDR: to decide which model to use, see Oxford Nanopore’s** `table of | ||
| basecalling | ||
| models <https://github.com/nanoporetech/dorado/?tab=readme-ov-file#decoding-dorado-model-names>`__. | ||
| The names of Dorado models are structured with each segment | ||
| corresponding to a different aspect of the model separated by | ||
| underscores. | ||
| For example, the model ``[email protected]`` can be | ||
| decoded as follows: | ||
| Analyte Type (``dna``): | ||
| - For DNA sequencing, it is represented as dna. If you are using a | ||
| Direct RNA Sequencing Kit, this will be rna002 or rna004, | ||
| depending on the kit. | ||
| Pore Type (``r10.4.1``): | ||
| - The type of flow cell used. | ||
| Chemistry Type (``e8.2``): | ||
| - The chemistry type, which corresponds to the kit used for | ||
| sequencing. For example, Kit 14 chemistry is denoted by e8.2 and | ||
| Kit 10 or Kit 9 are denoted by e8. | ||
| Translocation Speed (``400bps``): | ||
| - The speed of translocation selected at the run setup in MinKNOW | ||
| Model Type (``hac``): | ||
| - The size of the model, where larger models yield more accurate | ||
| basecalls but take more time. The three types of models are fast, | ||
| hac, and sup. The fast model is the quickest, sup is the most | ||
| accurate, and hac provides a balance between speed and accuracy. | ||
| Model Version Number (``v4.3.0``): | ||
| - The version of the model. Model updates are regularly released, | ||
| and higher version numbers typically signify greater accuracy. | ||
| ]]></help> | ||
| </tool> |
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| <tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> | ||
| <description>converter for raw Oxford Nanopore data</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="requirements"/> | ||
| <command><![CDATA[ | ||
| mkdir input_fast5 | ||
| && | ||
| tar -xf '$fast5_in' -C input_fast5 | ||
| && | ||
| pod5 convert fast5 | ||
| --threads \${GALAXY_SLOTS:-4} | ||
| --recursive | ||
| --output output.pod5 | ||
| input_fast5 | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive."/> | ||
| </inputs> | ||
| <outputs> | ||
| <!-- FIXME: add pod5 datatype to Galaxy and change here. | ||
| https://github.com/galaxyproject/galaxy/pull/18419 --> | ||
| <data format="binary" name="pod5_out" label="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/> | ||
| <output name="pod5_out" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size value="519736" delta="50000"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/> | ||
| <output name="pod5_out" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size value="950136" delta="90000"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| Convert fast5 to `pod5 <https://github.com/nanoporetech/pod5-file-format>`__ for basecalling with Dorado. | ||
| Combine all your fast5 files into a single tar archive, and optionally | ||
| compress the archive with Gzip, Bzip2 or XZ, before uploading it to | ||
| Galaxy. | ||
| ]]></help> | ||
| </tool> |
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| <macros> | ||
| <!-- UPDATING: pull the latest container and check the version. Update both tokens. You MUST also update the model list. See README.md for more. --> | ||
| <token name="@VERSION@">0.7.1+80da5f5</token> | ||
| <token name="@CONTAINER_HASH@">1c65eb070a9fc1d88710c4dc09b06541f96fdd28</token> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container> | ||
| </requirements> | ||
| </xml> | ||
| <xml name="xrefs"> | ||
| <xrefs> | ||
| <xref type="bio.tools">dorado</xref> | ||
| </xrefs> | ||
| </xml> | ||
| </macros> |
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| ../tool-data/dorado_models.loc.sample |
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