Mercurial > repos > iuc > busco
changeset 22:e5c372c91e46 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58
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--- a/busco.xml Fri Aug 30 15:19:56 2024 +0000 +++ b/busco.xml Tue Oct 29 14:13:47 2024 +0000 @@ -1,5 +1,5 @@ -<tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>assess genome assembly and annotation completeness</description> +<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>Assess genome assembly and annotation completeness</description> <macros> <import>macros.xml</import> </macros> @@ -54,7 +54,6 @@ #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus': ${busco_mode.use_augustus.long} --augustus - #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin': --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}' #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': @@ -84,9 +83,9 @@ #end if -]]> </command> +]]></command> <inputs> - <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." /> + <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."/> <conditional name="lineage_conditional"> <param name="selector" type="select" label="Lineage data source"> <option value="download">Download lineage data</option> @@ -95,7 +94,7 @@ <when value="cached"> <param name="cached_db" label="Cached database with lineage" type="select"> <options from_data_table="busco_database"> - <validator message="No BUSCO database is available" type="no_options" /> + <validator message="No BUSCO database is available" type="no_options"/> </options> </param> </when> @@ -113,7 +112,6 @@ <option value="augustus">Augustus</option> <option value="metaeuk">Metaeuk</option> <option value="miniprot" selected="true">Miniprot</option> - </param> <when value="metaeuk"/> <when value="miniprot"/> @@ -124,24 +122,23 @@ <option value="builtin">Use another predefined species model</option> <option value="history">Use a custom species model</option> </param> - <when value="no" /> + <when value="no"/> <when value="history"> - <param name="augustus_model" type="data" format="augustus" label="Augustus model" /> + <param name="augustus_model" type="data" format="augustus" label="Augustus model"/> </when> <when value="builtin"> <param name="augustus_species" type="select" label="Augustus species model"> - <expand macro="augustus_species" /> + <expand macro="augustus_species"/> </param> </when> </conditional> - <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" /> + <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"/> </when> </conditional> </when> - <when value="tran" /> - <when value="prot" /> + <when value="tran"/> + <when value="prot"/> </conditional> - <conditional name="lineage"> <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage"> <option value="auto_detect">Auto-detect</option> @@ -156,7 +153,7 @@ </when> <when value="select_lineage"> <param argument="--lineage_dataset" type="select" label="Lineage"> - <expand macro="lineages" /> + <expand macro="lineages"/> </param> </when> </conditional> @@ -169,8 +166,8 @@ </param> <section name="adv" title="Advanced Options" expanded="False"> - <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> - <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> + <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches."/> + <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/> <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/> </section> </inputs> @@ -179,7 +176,7 @@ <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> <filter>outputs and 'short_summary' in outputs</filter> </data> - <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" /> + <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/> <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"> <filter>outputs and 'missing' in outputs</filter> </data> @@ -193,148 +190,148 @@ <tests> <test expect_num_outputs="4"> - <param name="input" value="genome.fa" /> + <param name="input" value="genome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="geno" /> + <param name="mode" value="geno"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="augustus" /> + <param name="use_augustus_selector" value="augustus"/> </conditional> </conditional> - <param name="outputs" value="short_summary,missing,gff" /> + <param name="outputs" value="short_summary,missing,gff"/> <output name="busco_sum"> <assert_contents> <has_text text="# BUSCO version is: @TOOL_VERSION@"/> <has_text text="Gene predictor used: augustus"/> </assert_contents> </output> - <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/> <output name="busco_gff"> <assert_contents> <has_n_lines n="1"/> - <has_text text="##gff-version 3" /> + <has_text text="##gff-version 3"/> </assert_contents> </output> <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/> </test> <test expect_num_outputs="5"> - <param name="input" value="proteome.fa" /> + <param name="input" value="proteome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="prot" /> + <param name="mode" value="prot"/> </conditional> - <param name="outputs" value="short_summary,missing,image,gff" /> + <param name="outputs" value="short_summary,missing,image,gff"/> <output name="busco_sum"> <assert_contents> <has_text text="# BUSCO version is: @TOOL_VERSION@"/> - <has_text text="BUSCO was run in mode: proteins" /> + <has_text text="BUSCO was run in mode: proteins"/> </assert_contents> </output> - <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" /> - <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" /> - <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> + <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10"/> + <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10"/> + <output name="summary_image" file="proteome_results/summary.png" compare="sim_size"/> <output name="busco_gff"> <assert_contents> <has_n_lines n="1"/> - <has_text text="##gff-version 3" /> + <has_text text="##gff-version 3"/> </assert_contents> </output> </test> <test expect_num_outputs="5"> - <param name="input" value="transcriptome.fa" /> + <param name="input" value="transcriptome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="tran" /> + <param name="mode" value="tran"/> </conditional> - <param name="outputs" value="short_summary,missing,image,gff" /> + <param name="outputs" value="short_summary,missing,image,gff"/> <output name="busco_sum"> <assert_contents> - <has_text text="BUSCO was run in mode: euk_tran" /> + <has_text text="BUSCO was run in mode: euk_tran"/> </assert_contents> </output> - <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> - <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> - <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> - <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> + <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6"/> + <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6"/> + <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size"/> + <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff"/> </test> <test expect_num_outputs="3"> - <param name="input" value="genome.fa" /> + <param name="input" value="genome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="geno" /> + <param name="mode" value="geno"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="augustus" /> + <param name="use_augustus_selector" value="augustus"/> <conditional name="aug_prediction"> - <param name="augustus_mode" value="builtin" /> - <param name="augustus_species" value="human" /> + <param name="augustus_mode" value="builtin"/> + <param name="augustus_species" value="human"/> </conditional> </conditional> </conditional> - <param name="outputs" value="short_summary,gff" /> + <param name="outputs" value="short_summary,gff"/> <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10"> <assert_contents> <has_text text="# Gene predictor used: augustus"/> </assert_contents> </output> - <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/> <output name="busco_gff"> <assert_contents> <has_n_lines n="1"/> - <has_text text="##gff-version 3" /> + <has_text text="##gff-version 3"/> </assert_contents> </output> </test> <test expect_num_outputs="3"> - <param name="input" value="genome.fa" /> + <param name="input" value="genome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="geno" /> + <param name="mode" value="geno"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="augustus" /> + <param name="use_augustus_selector" value="augustus"/> <conditional name="aug_prediction"> - <param name="augustus_mode" value="history" /> - <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> + <param name="augustus_mode" value="history"/> + <param name="augustus_model" value="local.tar.gz" ftype="augustus"/> </conditional> </conditional> </conditional> - <param name="outputs" value="short_summary,missing" /> + <param name="outputs" value="short_summary,missing"/> <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10"> <assert_contents> <has_text text="# Gene predictor used: augustus"/> <has_text text="# BUSCO version is: @TOOL_VERSION@"/> </assert_contents> </output> - <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> - <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" /> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/> + <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/> </test> <test expect_num_outputs="5"> - <param name="input" value="genome.fa" /> + <param name="input" value="genome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="geno" /> + <param name="mode" value="geno"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="metaeuk" /> + <param name="use_augustus_selector" value="metaeuk"/> </conditional> </conditional> - <param name="outputs" value="short_summary,missing,image,gff" /> + <param name="outputs" value="short_summary,missing,image,gff"/> <output name="busco_sum"> <assert_contents> <has_text text="# Gene predictor used: metaeuk"/> @@ -353,21 +350,21 @@ </assert_contents> </output> <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/> - <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" /> + <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/> </test> <test expect_num_outputs="5"> - <param name="input" value="genome.fa" /> + <param name="input" value="genome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="auto_detect" /> - <param name="auto_lineage" value="--auto-lineage" /> + <param name="lineage_mode" value="auto_detect"/> + <param name="auto_lineage" value="--auto-lineage"/> </conditional> <conditional name="busco_mode"> - <param name="mode" value="geno" /> + <param name="mode" value="geno"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="metaeuk" /> + <param name="use_augustus_selector" value="metaeuk"/> </conditional> </conditional> - <param name="outputs" value="short_summary,missing,image,gff" /> + <param name="outputs" value="short_summary,missing,image,gff"/> <output name="busco_sum"> <assert_contents> <has_text text="Gene predictor used: metaeuk"/> @@ -385,22 +382,22 @@ <has_text text="The lineage dataset is: eukaryota_odb10"/> </assert_contents> </output> - <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> - <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> + <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/> + <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff"/> </test> <test expect_num_outputs="3"> - <param name="input" value="genome.fa" /> + <param name="input" value="genome.fa"/> <conditional name="lineage"> - <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="arthropoda_odb10" /> + <param name="lineage_mode" value="select_lineage"/> + <param name="lineage_dataset" value="arthropoda_odb10"/> </conditional> - <param name="outputs" value="short_summary,gff" /> + <param name="outputs" value="short_summary,gff"/> <output name="busco_sum"> <assert_contents> <has_text text="# Gene predictor used: miniprot"/> </assert_contents> </output> - <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" /> + <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/> <output name="busco_table" file="genome_results_miniprot/full_table"> <assert_contents> <has_text text="# BUSCO version is: @TOOL_VERSION@"/> @@ -412,7 +409,7 @@ <help><![CDATA[ -BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs +BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs -------------------------------------------------------------------------------------------------------------- Interpreting the results @@ -432,11 +429,11 @@ is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples is what you will be aiming for. -For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_ +For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_ . .. _BUSCO: http://busco.ezlab.org/ - ]]> </help> - <expand macro="citations" /> + ]]></help> + <expand macro="citations"/> </tool>
--- 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">
--- 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 @@ -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 @@ -509,7 +509,7 @@ 93535at6656 Missing 93797at6656 Missing 94054at6656 Missing -94238at6656 Complete sample 38486 34764 - 60.7 116 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1 +94238at6656 Complete sample 38486 34764 - 60.7 117 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing
--- 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 @@ -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 100070at6656
--- 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
--- 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
--- 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 @@ -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 100070at6656
--- 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 @@ -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 @@ -509,7 +509,7 @@ 93535at6656 Missing 93797at6656 Missing 94054at6656 Missing -94238at6656 Complete sample 35679 34845 - 60.7 116 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1 +94238at6656 Complete sample 35679 34845 - 60.7 117 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing
--- 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
--- 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 @@ -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 Score Length OrthoDB url Description 774at6656 Missing @@ -86,7 +86,7 @@ 22098at6656 Missing 22148at6656 Missing 22358at6656 Missing -22364at6656 Complete BUSCOaEOG7B0HST 1355.6 788 https://v10-1.orthodb.org/?query=22364at6656 Importin repeat 4 +22364at6656 Complete BUSCOaEOG7B0HST 1355.6 789 https://v10-1.orthodb.org/?query=22364at6656 Importin repeat 4 22468at6656 Missing 22611at6656 Missing 22887at6656 Missing
--- 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 @@ -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 100070at6656
--- 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 @@ -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 Score Length OrthoDB url Description 774at6656 Missing @@ -86,7 +86,7 @@ 22098at6656 Missing 22148at6656 Missing 22358at6656 Missing -22364at6656 Complete BUSCOaEOG7B0HST:0-2699 1355.6 788 https://v10-1.orthodb.org/?query=22364at6656 Importin repeat 4 +22364at6656 Complete BUSCOaEOG7B0HST:0-2699 1355.6 789 https://v10-1.orthodb.org/?query=22364at6656 Importin repeat 4 22468at6656 Missing 22611at6656 Missing 22887at6656 Missing
--- 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 @@ -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 100070at6656