# HG changeset patch
# User iuc
# Date 1761645489 0
# Node ID fc1f197b33ec942dddcddca6d6ad12476ab7c493
# Parent 18505fe2bdb1f8756f58776240a5a79a96382434
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
diff -r 18505fe2bdb1 -r fc1f197b33ec consensus.xml
--- a/consensus.xml Tue Sep 26 10:11:47 2023 +0000
+++ b/consensus.xml Tue Oct 28 09:58:09 2025 +0000
@@ -1,5 +1,5 @@
-
- Assembly polishing via neural networks
+
+ inference from a trained model and alignments.macros.xml
@@ -13,7 +13,7 @@
## Possibly new options bam_chunk and bam_workers. Should we be setting these?
## run
-medaka consensus
+medaka inference
## optional
--debug ## increase log level
--threads \${GALAXY_SLOTS:-4}
@@ -43,9 +43,7 @@
$tag_keep_missing
## required
alignment.bam ## bam
-'$out_result' ## output
-
-2>&1 | tee '$out_log'
+'$out_result' 2>&1 | tee log.txt
]]>
@@ -84,7 +82,7 @@
'result' in out
-
+
'log' in out
@@ -94,14 +92,14 @@
-
+
@@ -111,12 +109,12 @@
@@ -150,4 +148,4 @@
@REFERENCES@
]]>
-
\ No newline at end of file
+
diff -r 18505fe2bdb1 -r fc1f197b33ec macros.xml
--- a/macros.xml Tue Sep 26 10:11:47 2023 +0000
+++ b/macros.xml Tue Oct 28 09:58:09 2025 +0000
@@ -1,6 +1,6 @@
- 1.7.2
- 1
+ 2.1.1
+ 021.01
@@ -10,6 +10,7 @@
medaka
+ scipy
@@ -52,8 +53,8 @@
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@@ -61,71 +62,92 @@
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@@ -177,12 +199,12 @@
{pore}_{device}_{caller variant}_{caller version}
-For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model
+For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model
r941_prom_hac_g303 should be used with PromethION data and the high accuracy basecaller (termed "hac" in Guppy configuration files). Where a version of Guppy has been used without an exactly corresponding medaka model, the medaka model with the highest version equal to or less than the guppy version should be selected.
-
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]]>
`_ and `github `_.
+More information are available in the `github `_.
]]>