# HG changeset patch
# User galaxy-australia
# Date 1744700688 0
# Node ID 7a587728d74bb9de81a7bff3fdff51828d5a560e
# Parent 7ff7680fa7130902562215e2cb60b87d60f7f775
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 4e9b34685eeea001562ec29e1f10f5ee2eeca19c
diff -r 7ff7680fa713 -r 7a587728d74b README.md
--- 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 " ";
+}
+/^\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($0, /^\s*\{\s*"([^"]+)",/, m))
+ print " ";
+}
+/^\s*};/ { if (in_map) exit }' barcode_kits.cpp
+```
diff -r 7ff7680fa713 -r 7a587728d74b dorado_trimming.xml
--- a/dorado_trimming.xml Mon Nov 11 03:05:14 2024 +0000
+++ b/dorado_trimming.xml Tue Apr 15 07:04:48 2025 +0000
@@ -13,6 +13,7 @@
dorado trim
--verbose
+--sequencing-kit '${sequencing_kit}'
--threads "\${GALAXY_SLOTS}"
#if $trim_primers.no_trim_primers == 'dont_trim'
--no-trim-primers
@@ -32,13 +33,16 @@
]]>
+
+
+
-
+
@@ -50,6 +54,7 @@
+
+
+