# HG changeset patch
# User iuc
# Date 1761645471 0
# Node ID aa4b729e12b6ee02d4753d3c6d236ade371a503b
# Parent 271b1e495f16b46785b8913605651d8110640d35
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
diff -r 271b1e495f16 -r aa4b729e12b6 macros.xml
--- a/macros.xml Tue Sep 26 10:10:37 2023 +0000
+++ b/macros.xml Tue Oct 28 09:57:51 2025 +0000
@@ -1,6 +1,6 @@
- 1.7.2
- 1
+ 2.1.1
+ 0
21.01
@@ -10,6 +10,7 @@
medaka
+ scipy
@@ -52,8 +53,8 @@
-
@@ -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.
-
+
]]>
`_ and `github `_.
+More information are available in the `github `_.
]]>
diff -r 271b1e495f16 -r aa4b729e12b6 variant.xml
--- a/variant.xml Tue Sep 26 10:10:37 2023 +0000
+++ b/variant.xml Tue Oct 28 09:57:51 2025 +0000
@@ -1,4 +1,4 @@
-
+
decodes variant calls from medaka consensus output
macros.xml
@@ -12,7 +12,7 @@
#if $pool.pool_mode == "Yes":
## run
- medaka variant
+ medaka vcf
## optional
--debug
#if $regions
@@ -22,13 +22,13 @@
${ambig_ref}
${gvcf}
## required
- reference.fa
#for $current in $pool.inputs
'$current'
#end for
+ reference.fa
#elif $pool.pool_mode == "No":
## run
- medaka variant
+ medaka vcf
## optional
--debug
#if $regions
@@ -38,15 +38,13 @@
${ambig_ref}
${gvcf}
## required
+ '$pool.input'
reference.fa
- '$pool.input'
#end if
#if str($output_annotated.output_annotated_select) == 'false':
- '$out_variants' ##output
- 2>&1 | tee '$out_log'
+ '$out_variants' 2>&1 | tee log.txt
#else
- raw.vcf ##output of medaka variant
- 2>&1 | tee '$out_log'
+ raw.vcf 2>&1 | tee log.txt
&& ln -s '$output_annotated.in_bam' in.bam
&& ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
&& medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
@@ -98,7 +96,7 @@
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output_log_bool