Galaxy |

Changeset 0:1957c943df75 (2025-06-23)

Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 97793e41864a750b1c18c80b858c118e43ae8d97

added:
README.md
dorado_error_correct.xml
macros.xml
test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar
test-data/FAL00375_473bf0ed_0.ten_reads.bam
test-data/FAL00375_473bf0ed_0.ten_reads.pod5
test-data/SQK-RBK114_BC01_BC04_unclassified.pod5
test-data/corrected_reads.fasta
test-data/corrected_reads_paf.fasta
test-data/custom_primers.fasta.gz
test-data/dorado_models.loc
test-data/lsk109_single_read.fastqsanger.gz
test-data/overlaps.paf
test-data/reads.fq.gz
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 1957c943df75 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Jun 23 04:29:50 2025 +0000

[

@@ -0,0 +1,86 @@
+
+## 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
+```
+
+## Kits and Barcodes
+
+The list of acceptable kits and barcodes is not specified in the Dorado
+documentation.
+
+A list of all sequencing kits is in [`kits.cpp`](https://github.com/nanoporetech/dorado/blob/master/dorado/models/kits.cpp)
+
+Parsed into XML with the following GNU Awk program:
+
+```bash
+gawk '
+/namespace kit/ { in_kit_namespace = 1 }
+in_kit_namespace && /codes_map/ { in_map = 1; print "Entering kit::codes_map" }
+in_map && /^\s*\{/ {
+    if (match($0, /\{\s*KC::[A-Z0-9_]+,\s*\{\s*"([^"]+)"/, m))
+        print "            <option value=\"" m[1] "\">" m[1] "</option>";
+}
+/^\s*};/ {
+    if (in_map) {
+        print "Exiting kit::codes_map";
+        exit
+    }
+}' kits.cpp
+```
+
+I believe the allowed barcodes are in [`barcode_kits.cpp`](https://github.com/nanoporetech/dorado/blob/master/dorado/utils/barcode_kits.cpp).
+
+Parsed into XML with the following GNU Awk program:
+
+```bash
+gawk '
+/kit_info_map/ { in_map = 1 }
+in_map && /^\s*\{/ {
+    if (match($0, /^\s*\{\s*"([^"]+)",/, m))
+        print "            <option value=\"" m[1] "\">" m[1] "</option>";
+}
+/^\s*};/ { if (in_map) exit }' barcode_kits.cpp
+```

diff -r 000000000000 -r 1957c943df75 dorado_error_correct.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dorado_error_correct.xml Mon Jun 23 04:29:50 2025 +0000

[

@@ -0,0 +1,118 @@
+<tool id="dorado_error_correct" name="Dorado correct reads" version="@VERSION@+galaxy1" python_template_version="3.5" profile="24.1">
+    <description>improve the accuracy of nanopore sequencing reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+
+ln -s '$input_file' ./reads.fastq &&
+
+dorado correct
+--threads "\${GALAXY_SLOTS}"
+#if $use_model.model_selector == "model_file":
+   --model-path '${use_model.model.fields.path}'
+#end if
+
+#if $infer_type.infer_type_selector == "from_paf":
+--from-paf '$infer_type.input_paf'
+#end if
+
+reads.fastq
+
+#if $to_paf:
+   $to_paf > overlaps.paf
+#else:
+   > corrected_reads.fasta
+#end if
+
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fastq" label="Raw fastq file" help="Fastq file for improvement"/>
+        <conditional name="use_model">
+            <param name="model_selector" type="select" label="Use model file for read correction">
+                <option value="" selected="true">None</option>
+                <option value="model_file">Use model file for read correction</option>
+            </param>
+            <when value="model_file">
+                <expand macro="model_param"/>
+            </when>
+            <when value=""/>
+        </conditional>
+        <param name="to_paf" type="boolean" truevalue="--to-paf" label="This option produces paf as output"/>
+        <conditional name="infer_type">
+            <param name="infer_type_selector" type="select" label="Use paf file for mapping and inference">
+                <option value="" selected="true">None</option>
+                <option value="from_paf">from paf</option>
+            </param>
+            <when value="from_paf">
+                <param name="input_paf" type="data" format="paf" label="Input paf file"/>
+            </when>
+            <when value=""/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_fasta" format="fasta" label="Corrected reads from ${on_string} correct by ${tool.name} with model" from_work_dir="corrected_reads.fasta">
+            <filter>not to_paf</filter>
+        </data>
+        <data name="out_paf" format="paf" from_work_dir="overlaps.paf" label="${tool.name} ${on_string}, paf file">
+            <filter>to_paf</filter>
+        </data>
+    </outputs>
+    <tests>
+        
+        <test expect_num_outputs="1">
+            <param name="input_file" value="reads.fq.gz" ftype="fastq.gz"/>
+            <param name="model_selector" value="model_file"/>
+            <param name="model" value="herro-v1"/>
+            <output name="out_fasta" file="corrected_reads.fasta" ftype="fasta" compare="diff" lines_diff="50">
+                <assert_contents>
+                    <has_size size="361982" delta="100"/>
+                    <has_n_lines n="12"/>
+                </assert_contents>
+            </output>
+        </test>
+        
+        <test expect_num_outputs="1">
+            <param name="input_file" value="reads.fq.gz" ftype="fastq.gz"/>
+            <param name="to_paf" value="true"/>
+            <output name="out_paf" file="overlaps.paf" ftype="paf" compare="diff" lines_diff="50">
+                <assert_contents>
+                    <has_size size="254" delta="10"/>
+                </assert_contents>
+            </output>
+        </test>
+        
+        <test expect_num_outputs="1">
+            <param name="input_file" value="reads.fq.gz" ftype="fastq.gz"/>
+            <conditional name="infer_type">
+                <param name="infer_type_selector" value="from_paf"/>
+                <param name="input_paf" value="overlaps.paf"/>
+            </conditional>
+            <output name="out_fasta" file="corrected_reads_paf.fasta" ftype="fasta" compare="diff" lines_diff="5">
+                <assert_contents>
+                    <has_size size="273" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Dorado supports single-read error correction with the integration of the HERRO algorithm.
+HERRO uses all-vs-all alignment followed by haplotype-aware correction using
+a deep learning model to achieve higher single-read accuracies.
+The corrected reads are primarily useful for generating de novo assemblies of diploid organisms
+using Oxford Nanopore’s open source
+`Dorado <https://github.com/nanoporetech/dorado/>`__ basecaller.
+
+Dorado correct only supports FASTQ(.gz) as the input and generates a FASTA file as output.
+The input can be uncompressed or compressed with bgz.
+
+Dorado Correct now also provides a feature to run mapping (CPU-only stage) and inference (GPU-intensive stage) individually.
+This enables separation of the CPU and GPU heavy stages into individual steps which can even be run on different nodes with appropriate compute characteristics.
+Gzipped PAF is currently not supported for the --from-paf option.
+
+
+    ]]></help>
+    <expand macro="citation"/>
+</tool>

diff -r 000000000000 -r 1957c943df75 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jun 23 04:29:50 2025 +0000

b'@@ -0,0 +1,163 @@\n+<macros>\n+ \n+ <token name="@VERSION@">0.9.5+bd7fb217</token>\n+ <token name="@CONTAINER_HASH@">268dcb4cd02093e75cdc58821f8b93719c4255ed</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container>\n+ </requirements>\n+ </xml>\n+ <xml name="xrefs">\n+ <xrefs>\n+ <xref type="bio.tools">dorado</xref>\n+ </xrefs>\n+ </xml>\n+ <xml name="citation">\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{dorado,\n+ title = {Dorado},\n+ author = {{Oxford Nanopore}},\n+ year = {2024},\n+ url = {https://github.com/nanoporetech/dorado/},\n+ }\n+ </citation>\n+ </citations>\n+ </xml>\n+ <xml name="model_param">\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+ </xml>\n+ <xml name="barcode_kits">\n+ <option value="EXP-NBD103">EXP-NBD103</option>\n+ <option value="EXP-NBD104">EXP-NBD104</option>\n+ <option value="EXP-NBD114-24">EXP-NBD114-24</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-MAB114-24">SQK-MAB114-24</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</option>\n+ <option value="SQK-RBK110-96">SQK-RBK110-96</option>\n+ <option value="SQK-RBK111-24">SQK-RBK111-24</option>\n+ <option value="SQK-RBK111-96">SQK-RBK111-96</option>\n+ <option value="SQK-RBK114-24">SQK-RBK114-24</option>\n+ <option value="SQK-RBK114-96">SQK-RBK114-96</option>\n+ <option value="SQK-RLB001">SQK-RLB001</option>\n+ <option value="SQK-RPB004">SQK-RPB004</option>\n+ <option value="SQK-RPB114-24">SQK-RPB114-24</option>\n+ <option value="TWIST-16-UDI">TWIST-16-UDI</option>\n+ <option value="TWIST-96A-UDI">TWIST-96A-UDI</option>\n+ <option value="VSK-PTC001">VSK-PTC001</option>\n+ <option value="VSK-VMK001">VSK-VMK001</option>\n+ <option value="VSK-VMK004">VSK-VMK004</option>\n+ <option value="VSK-VPS001">VSK-VPS001</option>\n+ </xml>\n+ <xml name="sequencing_kits">\n+ <option value="SQK-16S024">SQK-16S024</option>\n+ <option value="SQK-16S114-24-260">SQK-16S114-24-260</option>\n+ <optio'..b'option>\n+ <option value="SQK-LSK114-260">SQK-LSK114-260</option>\n+ <option value="SQK-LSK114-XL">SQK-LSK114-XL</option>\n+ <option value="SQK-LSK114" selected="true">SQK-LSK114</option>\n+ <option value="SQK-LWB001">SQK-LWB001</option>\n+ <option value="SQK-LWP001">SQK-LWP001</option>\n+ <option value="SQK-MLK111-96-XL">SQK-MLK111-96-XL</option>\n+ <option value="SQK-MLK114-96-XL-260">SQK-MLK114-96-XL-260</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-NBD112-24">SQK-NBD112-24</option>\n+ <option value="SQK-NBD112-96">SQK-NBD112-96</option>\n+ <option value="SQK-NBD114-24-260">SQK-NBD114-24-260</option>\n+ <option value="SQK-NBD114-24">SQK-NBD114-24</option>\n+ <option value="SQK-NBD114-96-260">SQK-NBD114-96-260</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-PCB114-24-260">SQK-PCB114-24-260</option>\n+ <option value="SQK-PCB114-24">SQK-PCB114-24</option>\n+ <option value="SQK-PCS108">SQK-PCS108</option>\n+ <option value="SQK-PCS109">SQK-PCS109</option>\n+ <option value="SQK-PCS111">SQK-PCS111</option>\n+ <option value="SQK-PCS114-260">SQK-PCS114-260</option>\n+ <option value="SQK-PCS114">SQK-PCS114</option>\n+ <option value="SQK-PSK004">SQK-PSK004</option>\n+ <option value="SQK-RAB201">SQK-RAB201</option>\n+ <option value="SQK-RAB204">SQK-RAB204</option>\n+ <option value="SQK-RAD002">SQK-RAD002</option>\n+ <option value="SQK-RAD003">SQK-RAD003</option>\n+ <option value="SQK-RAD004">SQK-RAD004</option>\n+ <option value="SQK-RAD112">SQK-RAD112</option>\n+ <option value="SQK-RAD114-260">SQK-RAD114-260</option>\n+ <option value="SQK-RAD114">SQK-RAD114</option>\n+ <option value="SQK-RAS201">SQK-RAS201</option>\n+ <option value="SQK-RBK001">SQK-RBK001</option>\n+ <option value="SQK-RBK004">SQK-RBK004</option>\n+ <option value="SQK-RBK110-96">SQK-RBK110-96</option>\n+ <option value="SQK-RBK111-24">SQK-RBK111-24</option>\n+ <option value="SQK-RBK111-96">SQK-RBK111-96</option>\n+ <option value="SQK-RBK114-24-260">SQK-RBK114-24-260</option>\n+ <option value="SQK-RBK114-24">SQK-RBK114-24</option>\n+ <option value="SQK-RBK114-96-260">SQK-RBK114-96-260</option>\n+ <option value="SQK-RBK114-96">SQK-RBK114-96</option>\n+ <option value="SQK-RLB001">SQK-RLB001</option>\n+ <option value="SQK-RLI001">SQK-RLI001</option>\n+ <option value="SQK-RNA001">SQK-RNA001</option>\n+ <option value="SQK-RNA002">SQK-RNA002</option>\n+ <option value="SQK-RNA004-XL">SQK-RNA004-XL</option>\n+ <option value="SQK-RNA004">SQK-RNA004</option>\n+ <option value="SQK-RPB004">SQK-RPB004</option>\n+ <option value="SQK-RPB114-24-260">SQK-RPB114-24-260</option>\n+ <option value="SQK-RPB114-24">SQK-RPB114-24</option>\n+ <option value="SQK-ULK001">SQK-ULK001</option>\n+ <option value="SQK-ULK114-260">SQK-ULK114-260</option>\n+ <option value="SQK-ULK114">SQK-ULK114</option>\n+ <option value="VSK-PTC001">VSK-PTC001</option>\n+ <option value="VSK-VBK001">VSK-VBK001</option>\n+ <option value="VSK-VMK001">VSK-VMK001</option>\n+ <option value="VSK-VMK004">VSK-VMK004</option>\n+ <option value="VSK-VPS001">VSK-VPS001</option>\n+ <option value="VSK-VSK001">VSK-VSK001</option>\n+ <option value="VSK-VSK003">VSK-VSK003</option>\n+ <option value="VSK-VSK004">VSK-VSK004</option>\n+ </xml>\n+</macros>\n'

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diff -r 000000000000 -r 1957c943df75 test-data/corrected_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/corrected_reads.fasta Mon Jun 23 04:29:50 2025 +0000

b'@@ -0,0 +1,12 @@\n+>3855985e-bb9b-4df4-9825-cc08f373342b\n+CCCCTTGCTCTCTGTATTATTTCCTTCTGTTAGGGGGTTGGGGAGAGACATCTAGGATCCTTGGCGAAAAGAGGTGTTGAAAGGCAGAGGGGAGAGAATGGGGATAGGAGAGGGGAATAATTCACAGAAGATACACAAATAGCCAATATGAAAATTAAACCAAGCTCAATATCATTAGATTTAAGAAGTGCAAAATTCTTAAAGATACCTTCCTTGATTAGTTGTGCAAAAATAAAAACTTTGGACAACATCCAGTGTTAGTGGAGTAGAGAAATGAATATTCCCAATCACTCTTGATAGGAGTGTAAATTGGTGCAATCTCCCAGAAGGCAATTTCACTTTCACAGTTTTATATGTGCTTCCTCTTTGGCCCAGCAGTTTCACTTATAGGAATCTGTCCTACAGAAACATTAAACAAGCATATACAAATACAAGAACAAGAATGTTTATTAAAGCATTGTTGCATTAGAGTAAAAACAAAAACAATTACAATGCCTATCAATAAGGGGCCAGATAAGTCATTTGTGATTTATGTATACTATGGACTACTAGGCCCATGTTGCACTGAATACACATTCTGACATCAAAAAGATTAAGTTGAAAGGCAAGAGCTGCAGTGATGATCCCATCCATGTTTATTTTTTAAAAACTATATATGTTTATATACACATATTAAGTCTAGAAGGATCTAGTGGTGATCTTGGTGGGGAGGGGAGCAGGGAATTAAGAGGAGACAGGTATATTTTCCTTCTAATTTCATATACTTTTGTTGATTTTTAAAAATAGCAAACGGCCGGGTGCAGTGGCTCACACCTGTAATCCCAACACCTTGGGAGGCAGAGGAGGGCAGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAATATGGTGAAATGTTGTCTACTAAAAATACAAAAATTAGCCAGCCATGGTGGTGGGCACCTGTAATCCCAGCTACTCGGGGAGGCTGAGGCATGAGAATCACTTGAACCCGGAAGGTGGAGGTTGCAGTGAGCTGAGATCGCGCCACTGCACTCCAGCCTGGTCAACAGAATGAGACTCAGTCTTAAAAACAAAAACAAAAACACATAGAAAACATAAAAATAAAAATAGCAAACAGGTATTACTTCTATAATTAAGAAATGAGTAAAAACTGAAAAGAACAAAGGGAAACAGCACGTATAGAAGGCAAGCTCGCCCCAATTCACCTTGCATGTCCCTTGGCCCTGGCTCCCATCTAACCACAGAGAAGGGGTCAGAGACTCCAGTGCTGATGGGTTTTTTGCAGGGCATTGTAGCCCTAGAATATTTATGAGGCCTCCAGCAGCAATGAGTCCACGAAGGTTGCTGTGAGGATTAAATGAGATAATGTATTAAAGGCACTAGGAAAGTGGCTGGCTGGTGGTAAGCCCTCAATACTAACAGCTTTTCATTATTATTGTTATTATTTAAAAGCATCCTGTAGCCCAGTTCTGCAGGGTGCTCCTCTACTTTCCAGATCCCACTCACTGGCACAGATTTTAAGCATTCATGGCAGGTGTACAAATGCTTAGTTTCATGTCAGGGCTATAACTGCACTTAATTGCTAACAAAACCACTTCAAAAGAGCTGTTCACCTAAGGGATGCTTGTGCAGTTGGAAACCATGGCTACGTGGCTCTACTCAGCTTCAGAAGAGCATTACTTCCTTACCCATTAATGAATATATAAATAAATAATGATCACCATGCAAATGGCATATCTAAGCTTTTTGCAAATTTAAAGCAAAAATGGTTATTGGTCGCCCCTTTCATGTAAAAAAAAAAAGTTTTCAAAGTAGGTGGAAATAAGAAAGGGAATAAGTCTACGTTTTCTCCTCACCCCACCCCCTTGGAGAAGTCGGCCTCCTGCTGCCTCCGAATCCTTCCACTGAAGGTCGCCAGCATGGAGTTCATGGCTGTGCAATCAAATGAAACTCATGATGCAAATATATTGGGAAAAGAGAGAGAATTAAGTCTAGAGAGCCCTCATTTTATTATAAAATTATTGCTTTCTCTACCAAGGAGACTGAATAGAATAAAATTACAGGTACATGTGTACAATTGTACCTGTGGACCAAAAAAAAAAAAGGGGAGGGATTATTTGTATGCTAGAATGCATGCACAAAAAATAAACCAGATGGAAGAAATGATAAAGAAGGAGTTGCCTTTCAGGAACGACAGCTGCTTACAGCTGTGGGAGTTCCTGCAACAGTTTATATTGGCCATTTTGTTTCCTGGCTAAACTGATTGCATTATATCACGATTTTTTTTGACAACTTGAAAATCAGATTTTATTTCTCTCTCATAAACTCTTTTAATACCATTCTTAATAAGGAAGAAAAATGTTGCATGTTGTGACTGATAAATGGAAAACCTCATTTAGGATTTGGTTTACATATTCCAAATGGTAAAAGCTCAGTAACATGAAGATCGTGTGTACTCAGGCCAAGAAGATCACAGGATTGACAAATAACATACAGTCCTGGGCGCCCATTTGTGATTGTGCAAGATTTTCATTTTTGCTTTGTGATTAACACTGCCTCTGAACTGAGGAGTTACCATGCTAGCAAATCATTTGTCTATCACATCATCCACCTTCCCTCTCCTACAGAATTAACTCTCTTGATGGAACTGTAGGCATTGGGGACAAGTCCGCAGGGAAGCTATTTCTGAACAGGGATTCTCAAGTAGGTGGCTGTCGACTCATATGTCTCCCCTTCTCACACACTAACTAGTGTGGGTTTGTGTTTAAAAACAGACACCCACAGACACATAGATTTTCTCTTTCTCTCTCCATTTATTTTGAGCTAATCCCAAGGGAACTGTATCCTATTTATCTTTGTTCACCAAGTGCCTGGCCATCGAGGTTCAATAAATATTTGTTGAATGAATAAAAAGAAATCTGTTCTCTACTTCCTGGGGAAAGGAGTGAGCCTTAATCATGAGTAGAGTCTTTGTAATGTGAAGCCTTGGAAAAGCCATTTTTTTTTTTTTTTGGCCTGGGAGGGAAGCAAAGAAGGGAGTCAATGAAATTTGGAAACAGAACCTGTCCATCCACTTATCAATTTATTCAGCAAATAGTTATACACCGTCCTTGTTTTCATGGAATTCACAGTCTACTGGAGAGATGGATAAGAAGTAGAAGTCAGAAACAGAATGACAAATTATAAGTGCTATAAGGGAAGTAACTGGTTGTTGGAACAGACATTAATAGACAGGTTGACCAGAGAATCTCTTTAAGTAGACATCTGAGCTGAAACCTAAAGGATGAGAAGGTCAAGGAAGCAAGGAGCTAAGGAAGCAAGGAGCTTGATGTCATTAAGAATACCAAAAGCAAGTCAGTGGGGCCTAGCAGAGTGAGCAAGGAGAGAATGGTGTGCTAGAAGATGAAGGCTGGATGGGCCATGGTGAGGAATCTGGATTTTTATTCTGAGTTAAACTTCTTTATGAAAATGGAAAATTGAACTCTATAATTCTCAATATGGAACTTAGAACAGTACTTGACATGTAGCAAGTGATCAATAAATGTTAGCCATTATTTTACATGTATAGTACCCAAGTAAATTGGCAAGCCTTCGTCATAGTAATTGGAAAAAAATGATTAAAACTTTAGCAGTGAAAAAGATGGTCATTTACTTGATAAACATAGTTTTTATTTAGCAACTTTTCTTGTTTCTTTTTTTTTTTTTGGTATTTTTTTGTAGAGATGGGATTTCACCTTGTTGCTCAGGCTGGTCTTAAACTCCTGGGCTCAAGAGATCCACCCACCTAGGCCTCCCAAAGTGCTAGGATTACAGGCGTGTCCAGCCTATTTAGGAACCTTTTCCATACAACCAGTCAAATTCCAGACAAAGCTGGTCAGATTCCACTTACAAAAGGGAACACTCATTTCTTACTGATCCACTGATACTCAGTTTTC'..b'GCTATTTGGGAGGCTGAGGTGGGAGAATCACCTGACCCCAGGAGGTTGAGGCTGCAGTTAGCCATGATCACACCACCGCACTCCCGCCTAGGCAACAGGAGTGAGACCCTGTCTTAAAAAAAAGGAAAATCTTCGAGATTAGGGACGAGTGATCATCCAGCCATCACAAAGTATAAGACCTCACAAGAAGAAGGAGTGGCCGGGTGCGGTGGCTCACATCTGTAATCCCAGCACTGTGGGAGGCCGAGGCAGGTGGATCACGAGGTGAAGAGATCGAGACCATCCTGGCCAACATGGGGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCTGGGTGTGGTAGTGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGGGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCTGAGATCGCACCACTGCACTCCAGCCTGGGCAACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAGAGGAAGGAGAGAACAATGTTGCAAACAACTTACGCAATTCTTCTGGCAAATTGCTTGTTTTTAGAGTTCCTCTGGCTGGAGGGTTGCTAGGGGGTCTAGGCACAGCAGCTGGGGACGGAGGCTGGGGAACCTGTGGTCTCAGCTCTGCAGGGCACTCCAAGGACTCCCCAGGAGCACCAGCTCTATTAGGTGGCTGGTGATGTGGCTGGTCCCTAGAAAGGAATACATTTACAGTCAATTTTCATTCTTTACAAAGGCAAACCTTCAGGGACAGAAAGACTTTTAGAACTATGGGAAGATCCCAGTGGGCTCTCTCTCCTCTGCCTCTATTTCTTAACTGAGACAGAAGGAAGAGGGGAGCTCCATGGAGTTGTAGTCAATAAGCGTTTCAGCTGGCTGCCACATGTGAGGGCCTGTGCTCTGACTCCAAAGAGGGAAGCAGGATTTGATTTCTCTATTCAAGATTTGTTTAATTGGAAAAACAAGTCTCATGCACAGGGCAGACAAGGTCACCAACAAAACAAAGTAGTATGACAGGTGACACAGATGGTTGATGTTATAGGCATTCAGATAAAAAGACATGACTTTTAGCTCATAATAGGTAACATTTAATTATGTATCAAAAGGTAAAGAGGGCCATGTAGATTTAGAAGTATTTGTACTGTTGACATATAAATGGAAATCTGATTTTGAAGACCCTTTAAAGAAGTTGCTACCATATTAGATAGCATCTTTATTATTTTCGTTGCCAGTATTCCCACGAGCATTCTGCTGAGATGAACAATCAGATGACCTCGTGTGAGATTTGGAGGAGAGAAGGAAATGGAGAGCATGCTTCTGCCGCTTCTGTGGTTTCTGTCGGTAAGCACAGTGATGAGGTGCTGAGTTTTCCCCAGAAGGCCTCCCAGTGTCCTATTACCAGCTTCACAAGCGTCGAGGGCAGGGCATGGGCATCTATTGTTCACCAGTGGAGATCTATCTGGCACAGAACCGATCCAACCATTGCAGTGGTCACAGCGGTGTTGGCTTTCTGATTCTCGACCTTCCTGACCACCAGAGGAGACAGCCTCTTTGGTGGCCCTGTTCTGTGGTATTGTGCTAACCGGTGGTGGGACTAAAACTGTCTCTATAATGTTTTATTTCTTAAAAAAAAATTCTGAAGCAAATGTGACAATATGTTAACATTCTTAAAATCTGGGTAGTGGGAACATGGATGTTGTTATTTGTGGTGTGTTTGAAATTGTGTCATATTATAAATTTAAAAAAAATGTTTTGACTACAAAATCTCTATGTATATGCCCAGTTTTTGTAGATTGTTGCTTACGCTTTTCATATTTTTACCCAAGGAGTAATCAGGAATTCTAAAAGTCTTATGTAACAGGATTTAAAATAAAATTACACAGAATCTCAACTGTACTATATTTTGAAAATATGAATGATTAAGATTATTTTTTATATTTTTATTAATATAGAGAAAATAATTTCTATAAAATATGCTTTCAGCTAATGGGGGATCCCATTCCATATTTTTTTCTTTTTCTTTTTTTTTTTATTTCTCCAAGAAAAACTCATTCCAGTTCTTTTGCATTAAATTCTCTTATACCAAAAAAATTGTTTCAAAAGTTGCTTAGTTGTTATAGAAGATGATTGCTTATATGATAAAGAAATGTTAAGGCCTTGATAATATTCAAAAGCTTCTGTATAAAAACAATACCATGGAAATTAATGACAGAGTAAACTTTCTGAATTAAAGTTCTCTTTCAAACTATGAGTAAGAGGAGAATTAGCTGGCTTCTTTTTTCTTTTTTTTGAGGCAGGGTCTTGCTCTGTCACCCAGGCTCAATCACAGCTCACTGCAGCCTTGACCTCCTGGGCTCAGGTGATTTTCCCACCTTAGCCTCCTGAGTAGCTGGGACCACAGGCATGAGCCACCACACCTGGCTAATTTTTGTATTATTTTGGTAGAGATGGGATTTCGCCATGTTGCCCAAGCTGGTCACAAACTTCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTATGCCCAACCTCAGTTGGATGGGTTTGTGTGTATGTGTGTGTGTGTTTTGTTTGTTTTTTAGTTTTTGAGACAGAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCACGGCTCACTGCAGCCATGACCTCTTGTGCTCAGGCAGTTCTCCTGCCTCAGCCTCCTTAGTAGCTGGAACCACAGGTATGTGCCACCACACCCGGCTAATTTTTGTATTTTTTTGTAGAGATGGGTTTTCGCTATGTTGCCCAGGCTGGTCTCAAATTCCTGGGCTCAAACAATCCACCCACCTCTGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCAAGCCCAGCCTAGCTCCTCTACCTGAACTTATTTTTCATTATCCTAAAGTGATAAAATAGATCAAGAAGATCAGAACAGGCTTAAATTGATGCTATAAAACCAATTACTCTGTATTATCTTTGCAACTCTTTTGTAAGTCTAAAATTGTTTGAAAATAAAAGTTTATTTTAAAAATTACTATTCTCTTTCCTATTCAACACAAAACTTATTTCATAAAGATGCTTACATTTTGTTTATTTCCCTGGAATTTTAGATATTTCTTCTGTTAGAGTGCCTATCCTGCTATAAAATCACATTTTACCTAATTCCATTGTTTAAACTCCATGTATTTATGGTTTAGAAAAATAAGGGATCTGGCCCAGCACGGTGGCTAACACCCGTAATCCCAGCACTTTGGGAGGCTGATGTGGGTGGATCACTTGAGGCCAGGAGTTTGAAACCAGCCTGGGCAACAAAGTGAGACCCCTTCTCTGCAAAAAATAAAAAAATTAGCTGGGTGTGGTAGCGGGCGTCTGTAGTTCCAGCTACTCTTGGGAGGCTGAGGTTGGAAGATGGCTTGAGTGCAGGAGGCGAAGGTTTCAGTGAGTCGAGATCTCGCCACTGCACTCCACCCTAAGTGACAGAGTCAGATCCTGTCCCAAAAGAAAGAGAGAAAAAAAGAGATCTGTCTTGAAAGAAAATATGAGGGTTTGTGGGCTTCTGAGCAAAAGAGAAAGCAGGCATGTGCCTCTTCACCATTGTTAATAAAGTGGGCTTTTTTTCTTTCCATGAAATGTTCAAACTAATTACCGCTTTCTGTATTTCTGAAAAATCCACTCTAATAGGAACTTCATATTTTACTCTATGCTGTAAAAACAGAATCTAGTTTTACAGTGGTATATAAAAGTTGCTTTTGAGCAAAAGTAAACATTTAATCTACTTTCTTCCAAATATTGTCATAAATGAGGAAGCTCCATTTACATGAGTTTTACCTATATATTTTAGATCCATAAATTAAGAGAAAAGGAAAGTCCAAAGAGAATAAGGGAAAAAAAATGATTAAAGAGGCAGGGCACAGTGGCTCATGCCTGCAATCCCAGCACTTTGGGAGGCCGAGGCGAGACGATG\n'

diff -r 000000000000 -r 1957c943df75 test-data/corrected_reads_paf.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/corrected_reads_paf.fasta Mon Jun 23 04:29:50 2025 +0000

[

@@ -0,0 +1,3 @@
+[2025-05-09 07:19:50.605] [[32minfo[m] Running: "correct" "test-data/reads.fq" "--from-paf" "overlaps.paf"
+[2025-05-09 07:19:50.606] [[32minfo[m] Failed to load NVML
+[2025-05-09 07:19:50.606] [[31m[1merror[m] Input reads file test-data/reads.fq does not exist!

diff -r 000000000000 -r 1957c943df75 test-data/custom_primers.fasta.gz

Binary file test-data/custom_primers.fasta.gz has changed

diff -r 000000000000 -r 1957c943df75 test-data/dorado_models.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dorado_models.loc Mon Jun 23 04:29:50 2025 +0000

b'@@ -0,0 +1,98 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diff -r 000000000000 -r 1957c943df75 test-data/lsk109_single_read.fastqsanger.gz

Binary file test-data/lsk109_single_read.fastqsanger.gz has changed

diff -r 000000000000 -r 1957c943df75 test-data/overlaps.paf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlaps.paf Mon Jun 23 04:29:50 2025 +0000

[

@@ -0,0 +1,3 @@
+[2025-05-09 07:19:09.954] [[32minfo[m] Running: "correct" "test-data/reads.fq" "--to-paf"
+[2025-05-09 07:19:09.962] [[32minfo[m] Failed to load NVML
+[2025-05-09 07:19:09.965] [[31m[1merror[m] Input reads file test-data/reads.fq does not exist!

diff -r 000000000000 -r 1957c943df75 test-data/reads.fq.gz

Binary file test-data/reads.fq.gz has changed

diff -r 000000000000 -r 1957c943df75 test-data/reads_in_directories.tar.gz

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

diff -r 000000000000 -r 1957c943df75 tool-data/dorado_models.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dorado_models.loc.sample Mon Jun 23 04:29:50 2025 +0000

diff -r 000000000000 -r 1957c943df75 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Jun 23 04:29:50 2025 +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 1957c943df75 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Mon Jun 23 04:29:50 2025 +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