# HG changeset patch # User galaxy-australia # Date 1744700669 0 # Node ID 5e67ea3680049a98f69e04db7669d4f8e817507d # Parent 6942f170cc43bacd8a4a35ed66e8070b466e966a planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 4e9b34685eeea001562ec29e1f10f5ee2eeca19c diff -r 6942f170cc43 -r 5e67ea368004 README.md --- 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 " "; +} +/^\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 " "; +} +/^\s*};/ { if (in_map) exit }' barcode_kits.cpp +``` diff -r 6942f170cc43 -r 5e67ea368004 dorado.xml --- 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 @@ + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff -r 6942f170cc43 -r 5e67ea368004 macros.xml --- 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 @@ - - 0.8.2+6b413c9 - ae1d5e75f94041e4fd7af4a7ed6e6432b0eaea29 + + 0.9.5+bd7fb217 + 268dcb4cd02093e75cdc58821f8b93719c4255ed nanoporetech/dorado:sha@CONTAINER_HASH@ @@ -16,12 +17,139 @@ @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/}, + } + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 6942f170cc43 -r 5e67ea368004 test-data/custom_primers.fasta.gz Binary file test-data/custom_primers.fasta.gz has changed diff -r 6942f170cc43 -r 5e67ea368004 test-data/dorado_models.loc --- 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 @@ 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