Mercurial > repos > galaxy-australia > dorado
changeset 6:5e67ea368004 draft default tip
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 4e9b34685eeea001562ec29e1f10f5ee2eeca19c
| author | galaxy-australia |
|---|---|
| date | Tue, 15 Apr 2025 07:04:29 +0000 |
| parents | 6942f170cc43 |
| children | |
| files | README.md dorado.xml macros.xml test-data/custom_primers.fasta.gz test-data/dorado_models.loc tool-data/dorado_models.loc.sample |
| diffstat | 6 files changed, 372 insertions(+), 206 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Mon Nov 11 03:06:35 2024 +0000 +++ b/README.md Tue Apr 15 07:04:29 2025 +0000 @@ -46,3 +46,41 @@ > 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 +```
--- a/dorado.xml Mon Nov 11 03:06:35 2024 +0000 +++ b/dorado.xml Tue Apr 15 07:04:29 2025 +0000 @@ -41,45 +41,9 @@ <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> + <!-- dev note: the barcode kits are hardcoded in https://github.com/nanoporetech/dorado/blob/release-v0.9/dorado/utils/barcode_kits.cpp --> <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> + <expand macro="barcode_kits" /> </param> </inputs> <outputs>
--- a/macros.xml Mon Nov 11 03:06:35 2024 +0000 +++ b/macros.xml Tue Apr 15 07:04:29 2025 +0000 @@ -1,7 +1,8 @@ <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@">0.8.2+6b413c9</token> - <token name="@CONTAINER_HASH@">ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29</token> + <!-- 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@">0.9.5+bd7fb217</token> + <token name="@CONTAINER_HASH@">268dcb4cd02093e75cdc58821f8b93719c4255ed</token> <xml name="requirements"> <requirements> <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container> @@ -16,12 +17,139 @@ <citations> <citation type="bibtex"> @misc{dorado, - title = {Dorado}, - author = {{Oxford Nanopore}}, - year = {2024}, - url = {https://github.com/nanoporetech/dorado/}, - } + title = {Dorado}, + author = {{Oxford Nanopore}}, + year = {2024}, + url = {https://github.com/nanoporetech/dorado/}, + } </citation> </citations> </xml> + <xml name="barcode_kits"> + <option value="EXP-NBD103">EXP-NBD103</option> + <option value="EXP-NBD104">EXP-NBD104</option> + <option value="EXP-NBD114-24">EXP-NBD114-24</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-MAB114-24">SQK-MAB114-24</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> + </xml> + <xml name="sequencing_kits"> + <option value="SQK-16S024">SQK-16S024</option> + <option value="SQK-16S114-24-260">SQK-16S114-24-260</option> + <option value="SQK-16S114-24">SQK-16S114-24</option> + <option value="SQK-APK114">SQK-APK114</option> + <option value="SQK-CS9109">SQK-CS9109</option> + <option value="SQK-DCS108">SQK-DCS108</option> + <option value="SQK-DCS109">SQK-DCS109</option> + <option value="SQK-LRK001">SQK-LRK001</option> + <option value="SQK-LSK108">SQK-LSK108</option> + <option value="SQK-LSK109-XL">SQK-LSK109-XL</option> + <option value="SQK-LSK109">SQK-LSK109</option> + <option value="SQK-LSK110-XL">SQK-LSK110-XL</option> + <option value="SQK-LSK110">SQK-LSK110</option> + <option value="SQK-LSK111-XL">SQK-LSK111-XL</option> + <option value="SQK-LSK111">SQK-LSK111</option> + <option value="SQK-LSK112-XL">SQK-LSK112-XL</option> + <option value="SQK-LSK112">SQK-LSK112</option> + <option value="SQK-LSK114-260">SQK-LSK114-260</option> + <option value="SQK-LSK114-XL">SQK-LSK114-XL</option> + <option value="SQK-LSK114" selected="true">SQK-LSK114</option> + <option value="SQK-LWB001">SQK-LWB001</option> + <option value="SQK-LWP001">SQK-LWP001</option> + <option value="SQK-MLK111-96-XL">SQK-MLK111-96-XL</option> + <option value="SQK-MLK114-96-XL-260">SQK-MLK114-96-XL-260</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-NBD112-24">SQK-NBD112-24</option> + <option value="SQK-NBD112-96">SQK-NBD112-96</option> + <option value="SQK-NBD114-24-260">SQK-NBD114-24-260</option> + <option value="SQK-NBD114-24">SQK-NBD114-24</option> + <option value="SQK-NBD114-96-260">SQK-NBD114-96-260</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-PCB114-24-260">SQK-PCB114-24-260</option> + <option value="SQK-PCB114-24">SQK-PCB114-24</option> + <option value="SQK-PCS108">SQK-PCS108</option> + <option value="SQK-PCS109">SQK-PCS109</option> + <option value="SQK-PCS111">SQK-PCS111</option> + <option value="SQK-PCS114-260">SQK-PCS114-260</option> + <option value="SQK-PCS114">SQK-PCS114</option> + <option value="SQK-PSK004">SQK-PSK004</option> + <option value="SQK-RAB201">SQK-RAB201</option> + <option value="SQK-RAB204">SQK-RAB204</option> + <option value="SQK-RAD002">SQK-RAD002</option> + <option value="SQK-RAD003">SQK-RAD003</option> + <option value="SQK-RAD004">SQK-RAD004</option> + <option value="SQK-RAD112">SQK-RAD112</option> + <option value="SQK-RAD114-260">SQK-RAD114-260</option> + <option value="SQK-RAD114">SQK-RAD114</option> + <option value="SQK-RAS201">SQK-RAS201</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-RBK114-24-260">SQK-RBK114-24-260</option> + <option value="SQK-RBK114-24">SQK-RBK114-24</option> + <option value="SQK-RBK114-96-260">SQK-RBK114-96-260</option> + <option value="SQK-RBK114-96">SQK-RBK114-96</option> + <option value="SQK-RLB001">SQK-RLB001</option> + <option value="SQK-RLI001">SQK-RLI001</option> + <option value="SQK-RNA001">SQK-RNA001</option> + <option value="SQK-RNA002">SQK-RNA002</option> + <option value="SQK-RNA004-XL">SQK-RNA004-XL</option> + <option value="SQK-RNA004">SQK-RNA004</option> + <option value="SQK-RPB004">SQK-RPB004</option> + <option value="SQK-RPB114-24-260">SQK-RPB114-24-260</option> + <option value="SQK-RPB114-24">SQK-RPB114-24</option> + <option value="SQK-ULK001">SQK-ULK001</option> + <option value="SQK-ULK114-260">SQK-ULK114-260</option> + <option value="SQK-ULK114">SQK-ULK114</option> + <option value="VSK-PTC001">VSK-PTC001</option> + <option value="VSK-VBK001">VSK-VBK001</option> + <option value="VSK-VMK001">VSK-VMK001</option> + <option value="VSK-VMK004">VSK-VMK004</option> + <option value="VSK-VPS001">VSK-VPS001</option> + <option value="VSK-VSK001">VSK-VSK001</option> + <option value="VSK-VSK003">VSK-VSK003</option> + <option value="VSK-VSK004">VSK-VSK004</option> + </xml> </macros>
--- a/test-data/dorado_models.loc Mon Nov 11 03:06:35 2024 +0000 +++ b/test-data/dorado_models.loc Tue Apr 15 07:04:29 2025 +0000 @@ -1,80 +1,98 @@ -ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29_dna_r9.4.1_e8_fast@v3.4 ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29 dna_r9.4.1_e8_fast@v3.4 /models/dna_r9.4.1_e8_fast@v3.4 -ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29_dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1 ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29 dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1 /models/dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1 -ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29_dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0 ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29 dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0 /models/dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0 -ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29_dna_r9.4.1_e8_hac@v3.3 ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29 dna_r9.4.1_e8_hac@v3.3 /models/dna_r9.4.1_e8_hac@v3.3 -ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29_dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1 ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29 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