Mercurial > repos > galaxy-australia > dorado
changeset 0:63d8ecfcfab1 draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f
| author | galaxy-australia |
|---|---|
| date | Fri, 28 Jun 2024 03:39:11 +0000 |
| parents | |
| children | fc5b6491cf78 |
| files | README.md dorado.xml macros.xml test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar test-data/FAL00375_473bf0ed_0.ten_reads.pod5 test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 test-data/dorado_models.loc test-data/reads_in_directories.tar.gz tool-data/dorado_models.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 11 files changed, 377 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Jun 28 03:39:11 2024 +0000 @@ -0,0 +1,48 @@ + +## 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 +``` +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dorado.xml Fri Jun 28 03:39:11 2024 +0000 @@ -0,0 +1,186 @@ +<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="dna_r9.4.1_e8_fast@v3.4"/> + <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="dna_r9.4.1_e8_fast@v3.4"/> + <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="dna_r10.4.1_e8.2_400bps_hac@v4.3.0"/> + <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 ``dna_r10.4.1_e8.2_400bps_hac@v4.3.0`` 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jun 28 03:39:11 2024 +0000 @@ -0,0 +1,15 @@ +<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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jun 28 03:39:11 2024 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="dorado_models" comment_char="#"> + <columns>value, tool_version, name, path</columns> + <file path="tool-data/dorado_models.loc" /> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Jun 28 03:39:11 2024 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="dorado_models" comment_char="#"> + <columns>value, tool_version, name, path</columns> + <file path="${__HERE__}/test-data/dorado_models.loc" /> + </table> +</tables> \ No newline at end of file