Mercurial > repos > galaxy-australia > dorado_trimming
changeset 2:7a587728d74b 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 07:04:48 +0000 |
| parents | 7ff7680fa713 |
| children | |
| files | README.md dorado_trimming.xml macros.xml test-data/custom_primers.fasta.gz test-data/dorado_models.loc tool-data/dorado_models.loc.sample |
| diffstat | 6 files changed, 387 insertions(+), 174 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Mon Nov 11 03:05:14 2024 +0000 +++ b/README.md Tue Apr 15 07:04:48 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($0, /^\s*\{\s*"([^"]+)",/, m)) + print " <option value=\"" m[1] "\">" m[1] "</option>"; +} +/^\s*};/ { if (in_map) exit }' barcode_kits.cpp +```
--- a/dorado_trimming.xml Mon Nov 11 03:05:14 2024 +0000 +++ b/dorado_trimming.xml Tue Apr 15 07:04:48 2025 +0000 @@ -13,6 +13,7 @@ dorado trim --verbose +--sequencing-kit '${sequencing_kit}' --threads "\${GALAXY_SLOTS}" #if $trim_primers.no_trim_primers == 'dont_trim' --no-trim-primers @@ -32,13 +33,16 @@ ]]></command> <inputs> <param name="reads" type="data" format="bam,fastqsanger,unsorted.bam" label="Existing, basecalled DNA dataset" help="Note: this tool does not support trimming adaptors from RNA reads. These need to be removed during basecalling."/> + <param type="select" argument="--sequencing-kit" optional="false" label="Sequencing kit that was used for the experiment." help="Dorado determines which adapter and primer sequences to search for and trim based on the sequencing-kit specified. Note that by default the dorado software only supports adapter and primer trimming for kit14 sequencing kits."> + <expand macro="sequencing_kits"/> + </param> <conditional name="trim_primers"> <param argument="--no-trim-primers" type="select" label="Enable primer trimming" help="Selecting 'No' prevents the trimming of primer sequences. In this case only adapter sequences will be trimmed."> <option value="trim" selected="true">Yes</option> <option value="dont_trim">No</option> </param> <when value="trim"> - <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. 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."/> + <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/> </when> <when value="dont_trim"/> </conditional> @@ -50,6 +54,7 @@ <tests> <test expect_num_outputs="2"> <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/> + <param name="sequencing_kit" value="SQK-LSK109"/> <output name="out_bam" ftype="unsorted.bam"> <assert_contents> <has_size size="60725" delta="6000"/> @@ -63,6 +68,7 @@ </test> <test expect_num_outputs="2"> <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/> + <param name="sequencing_kit" value="SQK-LSK109"/> <param name="no_trim_primers" value="dont_trim"/> <output name="out_bam" ftype="unsorted.bam"> <assert_contents> @@ -77,6 +83,7 @@ </test> <test expect_num_outputs="2"> <param name="reads" value="lsk109_single_read.fastqsanger.gz" ftype="fastqsanger.gz"/> + <param name="sequencing_kit" value="SQK-LSK109"/> <param name="primer_sequences" value="custom_primers.fasta.gz" ftype="fasta.gz"/> <output name="out_bam" ftype="unsorted.bam"> <assert_contents> @@ -117,11 +124,15 @@ ---------------------- 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. +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. Note that if you use this option the normal primer +sequences built-in to the dorado software will not be searched for. + +Oxford Nanopore uses a non-standard FASTA format for this file. The format is +specified `here +<https://github.com/nanoporetech/dorado/blob/release-v0.9/documentation/CustomPrimers.md#custom-adapterprimer-file-format>`__. + RNA adapter trimming --------------------
--- a/macros.xml Mon Nov 11 03:05:14 2024 +0000 +++ b/macros.xml Tue Apr 15 07:04:48 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 03:05:14 2024 +0000 +++ b/test-data/dorado_models.loc Tue Apr 15 07:04:48 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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