# HG changeset patch
# User galaxy-australia
# Date 1730690875 0
# Node ID 1957f881bdf40c2ba5b0c8a422d066d5a664d52a
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 8f48f7ee85162eeaa9c0247c7bb7d699f84d6ca7
diff -r 000000000000 -r 1957f881bdf4 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Nov 04 03:27:55 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 update the loc file with models from the container with hash
+`1c65eb070a9fc1d88710c4dc09b06541f96fdd28`.
+
+```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.sample
+```
+
diff -r 000000000000 -r 1957f881bdf4 dorado_trimming.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dorado_trimming.xml Mon Nov 04 03:27:55 2024 +0000
@@ -0,0 +1,102 @@
+
+ for Oxford Nanopore (ONT) DNA reads
+
+ macros.xml
+
+
+
+ trimmed.bam
+
+&&
+
+dorado summary
+trimmed.bam
+> summary.tsv
+
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ `__ basecaller.
+
+This tool scans existing, basecalled datasets for adapter and/or primer
+sequences at either end, and trims any such found sequences.
+
+**If you have raw (un-basecalled) data, you can trim them during
+basecalling with the Dorado tool on Galaxy**.
+
+Note that if you intend to demultiplex the reads later, trimming
+adapters and primers may result in some portions of the flanking regions
+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 output of will always be unaligned records, regardless of whether
+the input is aligned/sorted or not.
+
+Custom primer trimming
+----------------------
+
+The software automatically searches for primer sequences used in Oxford
+Nanopore kits. However, you can specify an alternative set of primer
+sequences to search by adding a FASTA file of primer sequences in the
+**Custom primer sequences** option. 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.
+
+RNA adapter trimming
+--------------------
+
+Adapters for RNA002 and RNA004 kits are automatically trimmed during
+basecalling. However, unlike in DNA, the RNA adapter cannot be trimmed
+post-basecalling.
+ ]]>
+
+
diff -r 000000000000 -r 1957f881bdf4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Nov 04 03:27:55 2024 +0000
@@ -0,0 +1,27 @@
+
+
+ 0.8.2+6b413c9
+ ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29
+
+
+ nanoporetech/dorado:sha@CONTAINER_HASH@
+
+
+
+
+ dorado
+
+
+
+
+
+ @misc{dorado,
+ title = {Dorado},
+ author = {{Oxford Nanopore}},
+ year = {2024},
+ url = {https://github.com/nanoporetech/dorado/},
+ }
+
+
+
+
diff -r 000000000000 -r 1957f881bdf4 test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar
Binary file test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/FAL00375_473bf0ed_0.ten_reads.bam
Binary file test-data/FAL00375_473bf0ed_0.ten_reads.bam has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/FAL00375_473bf0ed_0.ten_reads.pod5
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diff -r 000000000000 -r 1957f881bdf4 test-data/SQK-RBK114_BC01_BC04_unclassified.pod5
Binary file test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/custom_primers.fasta.gz
Binary file test-data/custom_primers.fasta.gz has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_models.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dorado_models.loc Mon Nov 04 03:27:55 2024 +0000
@@ -0,0 +1,80 @@
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diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_trimming_test1.bam
Binary file test-data/dorado_trimming_test1.bam has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_trimming_test1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_trimming_test2.bam
Binary file test-data/dorado_trimming_test2.bam has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_trimming_test2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dorado_trimming_test2.tsv Mon Nov 04 03:27:55 2024 +0000
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diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_trimming_test3.bam
Binary file test-data/dorado_trimming_test3.bam has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/dorado_trimming_test3.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dorado_trimming_test3.tsv Mon Nov 04 03:27:55 2024 +0000
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diff -r 000000000000 -r 1957f881bdf4 test-data/lsk109_single_read.fastqsanger.gz
Binary file test-data/lsk109_single_read.fastqsanger.gz has changed
diff -r 000000000000 -r 1957f881bdf4 test-data/reads_in_directories.tar.gz
Binary file test-data/reads_in_directories.tar.gz has changed
diff -r 000000000000 -r 1957f881bdf4 tool-data/dorado_models.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dorado_models.loc.sample Mon Nov 04 03:27:55 2024 +0000
@@ -0,0 +1,80 @@
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diff -r 000000000000 -r 1957f881bdf4 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Nov 04 03:27:55 2024 +0000
@@ -0,0 +1,6 @@
+
+
+ value, tool_version, name, path
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 1957f881bdf4 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Mon Nov 04 03:27:55 2024 +0000
@@ -0,0 +1,6 @@
+
+
+ value, tool_version, name, path
+
+
+
\ No newline at end of file