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Changeset 22:e5c372c91e46 (2024-10-29)

Previous changeset 21:2babe6d5c561 (2024-08-30)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58

diff -r 2babe6d5c561 -r e5c372c91e46 busco.xml
--- a/busco.xml Fri Aug 30 15:19:56 2024 +0000
+++ b/busco.xml Tue Oct 29 14:13:47 2024 +0000

[

b'@@ -1,5 +1,5 @@\n-<tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n- <description>assess genome assembly and annotation completeness</description>\n+<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description>Assess genome assembly and annotation completeness</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -54,7 +54,6 @@\n #elif $busco_mode.use_augustus.use_augustus_selector == \'augustus\':\n ${busco_mode.use_augustus.long}\n --augustus\n-\n #if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'builtin\':\n --augustus_species \'${busco_mode.use_augustus.aug_prediction.augustus_species}\'\n #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'history\':\n@@ -84,9 +83,9 @@\n #end if\n \n \n-]]> </command>\n+]]></command>\n <inputs>\n- <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />\n+ <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set."/>\n <conditional name="lineage_conditional">\n <param name="selector" type="select" label="Lineage data source">\n <option value="download">Download lineage data</option>\n@@ -95,7 +94,7 @@\n <when value="cached">\n <param name="cached_db" label="Cached database with lineage" type="select">\n <options from_data_table="busco_database">\n- <validator message="No BUSCO database is available" type="no_options" />\n+ <validator message="No BUSCO database is available" type="no_options"/>\n </options>\n </param>\n </when>\n@@ -113,7 +112,6 @@\n <option value="augustus">Augustus</option>\n <option value="metaeuk">Metaeuk</option>\n <option value="miniprot" selected="true">Miniprot</option>\n-\n </param>\n <when value="metaeuk"/>\n <when value="miniprot"/>\n@@ -124,24 +122,23 @@\n <option value="builtin">Use another predefined species model</option>\n <option value="history">Use a custom species model</option>\n </param>\n- <when value="no" />\n+ <when value="no"/>\n <when value="history">\n- <param name="augustus_model" type="data" format="augustus" label="Augustus model" />\n+ <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>\n </when>\n <when value="builtin">\n <param name="augustus_species" type="select" label="Augustus species model">\n- <expand macro="augustus_species" />\n+ <expand macro="augustus_species"/>\n </param>\n </when>\n </conditional>\n- <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" />\n+ <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>\n '..b' <test expect_num_outputs="5">\n- <param name="input" value="genome.fa" />\n+ <param name="input" value="genome.fa"/>\n <conditional name="lineage">\n- <param name="lineage_mode" value="auto_detect" />\n- <param name="auto_lineage" value="--auto-lineage" />\n+ <param name="lineage_mode" value="auto_detect"/>\n+ <param name="auto_lineage" value="--auto-lineage"/>\n </conditional>\n <conditional name="busco_mode">\n- <param name="mode" value="geno" />\n+ <param name="mode" value="geno"/>\n <conditional name="use_augustus">\n- <param name="use_augustus_selector" value="metaeuk" />\n+ <param name="use_augustus_selector" value="metaeuk"/>\n </conditional>\n </conditional>\n- <param name="outputs" value="short_summary,missing,image,gff" />\n+ <param name="outputs" value="short_summary,missing,image,gff"/>\n <output name="busco_sum">\n <assert_contents>\n <has_text text="Gene predictor used: metaeuk"/>\n@@ -385,22 +382,22 @@\n <has_text text="The lineage dataset is: eukaryota_odb10"/>\n </assert_contents>\n </output>\n- <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />\n- <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />\n+ <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>\n+ <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff"/>\n </test>\n <test expect_num_outputs="3">\n- <param name="input" value="genome.fa" />\n+ <param name="input" value="genome.fa"/>\n <conditional name="lineage">\n- <param name="lineage_mode" value="select_lineage" />\n- <param name="lineage_dataset" value="arthropoda_odb10" />\n+ <param name="lineage_mode" value="select_lineage"/>\n+ <param name="lineage_dataset" value="arthropoda_odb10"/>\n </conditional>\n- <param name="outputs" value="short_summary,gff" />\n+ <param name="outputs" value="short_summary,gff"/>\n <output name="busco_sum">\n <assert_contents>\n <has_text text="# Gene predictor used: miniprot"/>\n </assert_contents>\n </output>\n- <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />\n+ <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/>\n <output name="busco_table" file="genome_results_miniprot/full_table">\n <assert_contents>\n <has_text text="# BUSCO version is: @TOOL_VERSION@"/>\n@@ -412,7 +409,7 @@\n <help><![CDATA[\n \n \n-BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs\n+BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs\n --------------------------------------------------------------------------------------------------------------\n \n Interpreting the results\n@@ -432,11 +429,11 @@\n is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples\n is what you will be aiming for.\n \n-For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_\n+For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_\n .\n \n .. _BUSCO: http://busco.ezlab.org/\n \n- ]]> </help>\n- <expand macro="citations" />\n+ ]]></help>\n+ <expand macro="citations"/>\n </tool>\n'

diff -r 2babe6d5c561 -r e5c372c91e46 macros.xml
--- a/macros.xml Fri Aug 30 15:19:56 2024 +0000
+++ b/macros.xml Tue Oct 29 14:13:47 2024 +0000

@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<macros>
-    <token name="@TOOL_VERSION@">5.7.1</token>
+    <token name="@TOOL_VERSION@">5.8.0</token>
     <token name="@VERSION_SUFFIX@">0</token>

     <xml name="citations">

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results/full_table
--- a/test-data/genome_results/full_table Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results/full_table Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results/missing_buscos_list
--- a/test-data/genome_results/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results/missing_buscos_list Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results/short_summary
--- a/test-data/genome_results/short_summary Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results/short_summary Tue Oct 29 14:13:47 2024 +0000

@@ -1,6 +1,6 @@
-# BUSCO version is: 5.7.1
+# BUSCO version is: 5.8.0
# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/7/a/3/dataset_7a33f452-1064-4b4a-943f-b0efef6a4a4a.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpmwpuw5w8/files/f/d/6/dataset_fd6995c7-d1df-43b9-b8be-7e62043550f0.dat
# BUSCO was run in mode: euk_genome_aug
# Gene predictor used: augustus

@@ -24,13 +24,13 @@

Dependencies and versions:
- hmmsearch: 3.1
- bbtools: 39.06
- makeblastdb: 2.15.0+
- tblastn: 2.15.0+
+ hmmsearch: 3.4
+ bbtools: None
+ makeblastdb: 2.16.0+
+ tblastn: 2.16.0+
augustus: 3.5.0
gff2gbSmallDNA.pl: None
new_species.pl: None
etraining: None
- python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
- busco: 5.7.1
+ python: sys.version_info(major=3, minor=10, micro=14, releaselevel='final', serial=0)
+ busco: 5.8.0

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results_metaeuk/full_table
--- a/test-data/genome_results_metaeuk/full_table Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results_metaeuk/full_table Tue Oct 29 14:13:47 2024 +0000

@@ -1,4 +1,4 @@
-# BUSCO version is: 5.7.1
+# BUSCO version is: 5.8.0
# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)
# Busco id Status Sequence Gene Start Gene End Strand Score Length OrthoDB url Description
774at6656 Missing
@@ -340,7 +340,7 @@
68939at6656 Missing
68961at6656 Missing
68981at6656 Missing
-68987at6656 Complete sample 40255 42070 + 122.8 266 https://v10-1.orthodb.org/?query=68987at6656 Nucleotidyl transferase domain
+68987at6656 Complete sample 40255 42070 + 122.8 267 https://v10-1.orthodb.org/?query=68987at6656 Nucleotidyl transferase domain
69201at6656 Missing
69238at6656 Missing
69284at6656 Missing
@@ -509,7 +509,7 @@
93535at6656 Missing
93797at6656 Missing
94054at6656 Missing
-94238at6656 Complete sample 35693 34845 - 60.6 116 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1
+94238at6656 Complete sample 35693 34845 - 60.6 117 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1
94263at6656 Missing
94304at6656 Missing
94473at6656 Missing

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results_metaeuk/missing_buscos_list
--- a/test-data/genome_results_metaeuk/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results_metaeuk/missing_buscos_list Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results_metaeuk/summary.png

Binary file test-data/genome_results_metaeuk/summary.png has changed

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results_metaeuk_auto/summary.png

Binary file test-data/genome_results_metaeuk_auto/summary.png has changed

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results_miniprot/full_table
--- a/test-data/genome_results_miniprot/full_table Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results_miniprot/full_table Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/genome_results_miniprot/out.gff
--- a/test-data/genome_results_miniprot/out.gff Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/genome_results_miniprot/out.gff Tue Oct 29 14:13:47 2024 +0000

@@ -0,0 +1,4 @@
+##gff-version 3
+sample miniprot mRNA 34843 35679 1341 - . ID=MP000459;Rank=1;Identity=0.9640;Positive=0.9856;Target=94238at6656_7220_0:000926 1 278
+sample miniprot CDS 34843 35679 1341 - 0 Parent=MP000459;Rank=1;Identity=0.9640;Target=94238at6656_7220_0:000926 1 278
+sample miniprot stop_codon 34843 34845 0 - 0 Parent=MP000459;Rank=1

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/proteome_results/full_table
--- a/test-data/proteome_results/full_table Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/proteome_results/full_table Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/proteome_results/missing_buscos_list
--- a/test-data/proteome_results/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/proteome_results/missing_buscos_list Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/proteome_results/summary.png

Binary file test-data/proteome_results/summary.png has changed

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/transcriptome_results/full_table
--- a/test-data/transcriptome_results/full_table Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/transcriptome_results/full_table Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/transcriptome_results/missing_buscos_list
--- a/test-data/transcriptome_results/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000
+++ b/test-data/transcriptome_results/missing_buscos_list Tue Oct 29 14:13:47 2024 +0000

diff -r 2babe6d5c561 -r e5c372c91e46 test-data/transcriptome_results/summary.png

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