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Changeset 0:63d8ecfcfab1 (2024-06-28)

Next changeset 1:fc5b6491cf78 (2024-07-22)

Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f

added:
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

diff -r 000000000000 -r 63d8ecfcfab1 README.md
--- /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
+```
+

diff -r 000000000000 -r 63d8ecfcfab1 dorado.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dorado.xml Fri Jun 28 03:39:11 2024 +0000

[

b'@@ -0,0 +1,186 @@\n+<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05">\n+ <description>basecaller for raw Oxford Nanopore data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="xrefs"/>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ln -s \'$pod5_file\' ./reads.pod5\n+\n+&&\n+\n+dorado basecaller\n+--trim \'${trim}\'\n+#if $kit_name\n+ --kit-name \'${kit_name}\'\n+#end if\n+\'${model.fields.path}\'\n+reads.pod5 \n+> calls.bam\n+\n+&& \n+\n+dorado summary\n+calls.bam \n+> summary.tsv\n+\n+ ]]></command>\n+ <inputs>\n+ \n+ <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."/>\n+ <param name="model" type="select" label="Basecalling model. See the Help section for info on model names.">\n+ <options from_data_table="dorado_models">\n+ \n+ <filter type="static_value" column="1" value="@CONTAINER_HASH@"/>\n+ </options>\n+ </param>\n+ <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.">\n+ <option value="all" selected="true">Any. Trim any detected adapters or primers.</option>\n+ <option value="primers"> Primers. Trim any detected adapters or primers, but if barcoding is enabled the barcode sequences will not be trimmed.</option>\n+ <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>\n+ <option value="none"> None. Nothing will be trimmed.</option>\n+ </param>\n+ <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.">\n+ <option value="EXP-NBD103">EXP-NBD103</option>\n+ <option value="EXP-NBD104">EXP-NBD104</option>\n+ <option value="EXP-NBD114">EXP-NBD114</option>\n+ <option value="EXP-NBD196">EXP-NBD196</option>\n+ <option value="EXP-PBC001">EXP-PBC001</option>\n+ <option value="EXP-PBC096">EXP-PBC096</option>\n+ <option value="SQK-16S024">SQK-16S024</option>\n+ <option value="SQK-16S114-24">SQK-16S114-24</option>\n+ <option value="SQK-LWB001">SQK-LWB001</option>\n+ <option value="SQK-MLK111-96-XL">SQK-MLK111-96-XL</option>\n+ <option value="SQK-MLK114-96-XL">SQK-MLK114-96-XL</option>\n+ <option value="SQK-NBD111-24">SQK-NBD111-24</option>\n+ <option value="SQK-NBD111-96">SQK-NBD111-96</option>\n+ <option value="SQK-NBD114-24">SQK-NBD114-24</option>\n+ <option value="SQK-NBD114-96">SQK-NBD114-96</option>\n+ <option value="SQK-PBK004">SQK-PBK004</option>\n+ <option value="SQK-PCB109">SQK-PCB109</option>\n+ <option value="SQK-PCB110">SQK-PCB110</option>\n+ <option value="SQK-PCB111-24">SQK-PCB111-24</option>\n+ <option value="SQK-PCB114-24">SQK-PCB114-24</option>\n+ <option value="SQK-RAB201">SQK-RAB201</option>\n+ <option value="SQK-RAB204">SQK-RAB204</option>\n+ <option value="SQK-RBK001">SQK-RBK001</option>\n+ <option value="SQK-RBK004">SQK-RBK004</optio'..b'\n+ <param name="model" value="dna_r9.4.1_e8_fast@v3.4"/>\n+ <param name="trim" value="all"/>\n+ <output name="out_bam" ftype="unsorted.bam">\n+ <assert_contents>\n+ <has_size size="10000" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_tsv" ftype="tsv">\n+ <assert_contents>\n+ <has_text text="00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ \n+ <test expect_num_outputs="2">\n+ <param name="pod5_file" value="FAL00375_473bf0ed_0.ten_reads.pod5"/>\n+ <param name="model" value="dna_r9.4.1_e8_fast@v3.4"/>\n+ <param name="trim" value="adapters"/>\n+ <output name="out_bam" ftype="unsorted.bam">\n+ <assert_contents>\n+ <has_size size="10000" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_tsv" ftype="tsv">\n+ <assert_contents>\n+ <has_text text="0072b26f-f37c-4517-afa7-621543ac2187"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ \n+ <test expect_num_outputs="2">\n+ <param name="pod5_file" value="SQK-RBK114_BC01_BC04_unclassified.pod5"/>\n+ <param name="model" value="dna_r10.4.1_e8.2_400bps_hac@v4.3.0"/>\n+ <param name="trim" value="all"/>\n+ <param name="kit_name" value="SQK-RBK114-96"/>\n+ <output name="out_bam" ftype="unsorted.bam">\n+ <assert_contents>\n+ <has_size size="10000" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_tsv" ftype="tsv">\n+ <assert_contents>\n+ <has_size size="1103e241-dd7f-43bc-ae19-9a3c6326ad83"/>\n+ <has_text text="SQK-RBK114-96_barcode04"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Basecall raw Nanopore data using Oxford Nanopore\xe2\x80\x99s open source\n+`dorado <https://github.com/nanoporetech/dorado/>`__ basecaller.\n+\n+The input is pod5 format. If you have older data in fast5 format, you\n+can convert them using the ``fast5 to pod5`` convert tool.\n+\n+Basecalling models\n+------------------\n+\n+**TLDR: to decide which model to use, see Oxford Nanopore\xe2\x80\x99s** `table of\n+basecalling\n+models <https://github.com/nanoporetech/dorado/?tab=readme-ov-file#decoding-dorado-model-names>`__.\n+\n+The names of Dorado models are structured with each segment\n+corresponding to a different aspect of the model separated by\n+underscores.\n+\n+For example, the model ``dna_r10.4.1_e8.2_400bps_hac@v4.3.0`` can be\n+decoded as follows:\n+\n+Analyte Type (``dna``):\n+ - For DNA sequencing, it is represented as dna. If you are using a\n+ Direct RNA Sequencing Kit, this will be rna002 or rna004,\n+ depending on the kit.\n+Pore Type (``r10.4.1``):\n+ - The type of flow cell used.\n+Chemistry Type (``e8.2``):\n+ - The chemistry type, which corresponds to the kit used for\n+ sequencing. For example, Kit 14 chemistry is denoted by e8.2 and\n+ Kit 10 or Kit 9 are denoted by e8.\n+Translocation Speed (``400bps``):\n+ - The speed of translocation selected at the run setup in MinKNOW\n+Model Type (``hac``):\n+ - The size of the model, where larger models yield more accurate\n+ basecalls but take more time. The three types of models are fast,\n+ hac, and sup. The fast model is the quickest, sup is the most\n+ accurate, and hac provides a balance between speed and accuracy.\n+Model Version Number (``v4.3.0``):\n+ - The version of the model. Model updates are regularly released,\n+ and higher version numbers typically signify greater accuracy.\n+\n+ ]]></help>\n+</tool>\n'

diff -r 000000000000 -r 63d8ecfcfab1 macros.xml
--- /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>
+    
+    <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>

diff -r 000000000000 -r 63d8ecfcfab1 test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar

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diff -r 000000000000 -r 63d8ecfcfab1 test-data/FAL00375_473bf0ed_0.ten_reads.pod5

Binary file test-data/FAL00375_473bf0ed_0.ten_reads.pod5 has changed

diff -r 000000000000 -r 63d8ecfcfab1 test-data/SQK-RBK114_BC01_BC04_unclassified.pod5

Binary file test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 has changed

diff -r 000000000000 -r 63d8ecfcfab1 test-data/dorado_models.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dorado_models.loc Fri Jun 28 03:39:11 2024 +0000

b'@@ -0,0 +1,58 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diff -r 000000000000 -r 63d8ecfcfab1 test-data/reads_in_directories.tar.gz

Binary file test-data/reads_in_directories.tar.gz has changed

diff -r 000000000000 -r 63d8ecfcfab1 tool-data/dorado_models.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dorado_models.loc.sample Fri Jun 28 03:39:11 2024 +0000

diff -r 000000000000 -r 63d8ecfcfab1 tool_data_table_conf.xml.sample
--- /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

diff -r 000000000000 -r 63d8ecfcfab1 tool_data_table_conf.xml.test
--- /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