# HG changeset patch # User iuc # Date 1699967017 0 # Node ID 2a5b8b9936bf48ea6512dc13c2a584db1f802317 # Parent 94170eee0ad899644248ae6501d2f12ff6bfbeea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 diff -r 94170eee0ad8 -r 2a5b8b9936bf busco.xml --- a/busco.xml Fri Apr 14 08:13:46 2023 +0000 +++ b/busco.xml Tue Nov 14 13:03:37 2023 +0000 @@ -35,6 +35,7 @@ --cpu \${GALAXY_SLOTS:-4} --evalue ${adv.evalue} --limit ${adv.limit} +--contig_break ${adv.contig_break} #if $lineage_conditional.selector == 'cached': --offline @@ -48,6 +49,7 @@ #else if $lineage.lineage_mode == "select_lineage": --lineage_dataset '${lineage.lineage_dataset}' #end if + #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': ${busco_mode.use_augustus.long} @@ -60,6 +62,12 @@ #end if #end if +#if str( $busco_mode.mode ) == "geno": + #if $busco_mode.miniprot: + --miniprot + #end if +#end if + #if $outputs and 'image' in $outputs: && mkdir BUSCO_summaries @@ -78,6 +86,7 @@ cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true #end if + ]]> @@ -102,6 +111,7 @@ + @@ -162,8 +172,10 @@
+
+ outputs and 'short_summary' in outputs @@ -178,7 +190,11 @@ outputs and 'gff' in outputs + + busco_mode['mode'] == 'geno' and busco_mode['miniprot'] + + @@ -244,7 +260,7 @@ - + @@ -252,6 +268,7 @@ + @@ -269,6 +286,8 @@ + + diff -r 94170eee0ad8 -r 2a5b8b9936bf macros.xml --- a/macros.xml Fri Apr 14 08:13:46 2023 +0000 +++ b/macros.xml Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ - 5.4.6 + 5.5.0 0 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/full_table --- a/test-data/genome_results/full_table Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results/full_table Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, 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 34764 38486 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 +94238at6656 Complete sample:34764-38486 34764 38486 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/full_table_cached --- a/test-data/genome_results/full_table_cached Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results/full_table_cached Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.6 +# BUSCO version is: 5.5.0 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194) # Busco id Status Sequence Gene Start Gene End Strand Score Length 860at2157 Missing diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/miniprot_1000.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/miniprot_1000.gff 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test-data/genome_results/missing_buscos_list --- a/test-data/genome_results/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/short_summary --- a/test-data/genome_results/short_summary Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results/short_summary Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_22.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmpbmq1q2c6/files/8/e/b/dataset_8eb218b1-f367-4315-9915-554c009808cb.dat # BUSCO was run in mode: euk_genome_aug # Gene predictor used: augustus @@ -26,10 +26,10 @@ Dependencies and versions: hmmsearch: 3.1 bbtools: 39.01 - makeblastdb: 2.13.0+ - tblastn: 2.13.0+ + makeblastdb: 2.14.0+ + tblastn: 2.14.0+ augustus: 3.5.0 gff2gbSmallDNA.pl: None new_species.pl: None etraining: None - busco: 5.4.4 + busco: 5.5.0 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/short_summary_cached --- a/test-data/genome_results/short_summary_cached Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results/short_summary_cached Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.4.6 +# BUSCO version is: 5.5.0 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194) -# Summarized benchmarking in BUSCO notation for file /tmp/tmpte_du6dt/files/000/dataset_1.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmpbmq1q2c6/files/3/3/0/dataset_330f49ed-7a6b-4380-870f-22494bb4b257.dat # BUSCO was run in mode: prok_genome # Gene predictor used: prodigal @@ -27,4 +27,4 @@ hmmsearch: 3.1 bbtools: 39.01 prodigal: 2.6.3 - busco: 5.4.6 + busco: 5.5.0 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/full_table --- a/test-data/genome_results_metaeuk/full_table Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results_metaeuk/full_table Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, 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://www.orthodb.org/v10?query=68987at6656 mannose-1-phosphate guanyltransferase alpha +68987at6656 Complete sample:40255-42070 40255 42070 + 122.8 266 https://www.orthodb.org/v10?query=68987at6656 mannose-1-phosphate guanyltransferase alpha 69201at6656 Missing 69238at6656 Missing 69284at6656 Missing @@ -509,7 +509,7 @@ 93535at6656 Missing 93797at6656 Missing 94054at6656 Missing -94238at6656 Complete sample 34845 35678 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 +94238at6656 Complete sample:35678-34845 34845 35678 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/missing_buscos_list --- a/test-data/genome_results_metaeuk/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results_metaeuk/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/short_summary --- a/test-data/genome_results_metaeuk/short_summary Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results_metaeuk/short_summary Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_28.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/1/d/2/dataset_1d20a949-adce-4511-8cab-345d59a61a05.dat # BUSCO was run in mode: euk_genome_met # Gene predictor used: metaeuk @@ -27,4 +27,4 @@ hmmsearch: 3.1 bbtools: 39.01 metaeuk: 6.a5d39d9 - busco: 5.4.4 + busco: 5.5.0 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/summary.png Binary file test-data/genome_results_metaeuk/summary.png has changed diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/full_table --- a/test-data/genome_results_metaeuk_auto/full_table Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results_metaeuk_auto/full_table Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) # Busco id Status Sequence Gene Start Gene End Strand Score Length 39650at2759 Missing @@ -131,7 +131,7 @@ 1041560at2759 Missing 1049599at2759 Missing 1051021at2759 Missing -1053181at2759 Complete sample 34845 35678 - 45.0 149 +1053181at2759 Complete sample:35678-34845 34845 35678 - 45.0 149 1057950at2759 Missing 1065019at2759 Missing 1076134at2759 Missing diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/missing_buscos_list --- a/test-data/genome_results_metaeuk_auto/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results_metaeuk_auto/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) # Busco id 1001705at2759 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/short_summary --- a/test-data/genome_results_metaeuk_auto/short_summary Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/genome_results_metaeuk_auto/short_summary Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) -# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_34.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/a/5/a/dataset_a5adf25d-f667-41d6-9472-f8661403e128.dat # BUSCO was run in mode: euk_genome_met # Gene predictor used: metaeuk @@ -27,5 +27,5 @@ hmmsearch: 3.1 bbtools: 39.01 prodigal: 2.6.3 - busco: 5.4.4 + busco: 5.5.0 metaeuk: 6.a5d39d9 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/summary.png Binary file test-data/genome_results_metaeuk_auto/summary.png has changed diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/full_table --- a/test-data/proteome_results/full_table Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/proteome_results/full_table Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) # Busco id Status Sequence Score Length OrthoDB url Description 774at6656 Missing diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/missing_buscos_list --- a/test-data/proteome_results/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/proteome_results/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/short_summary --- a/test-data/proteome_results/short_summary Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/proteome_results/short_summary Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_6.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/b/a/7/dataset_ba764d57-9365-4d54-a1f8-ac1350df0747.dat # BUSCO was run in mode: proteins ***** Results: ***** @@ -15,4 +15,4 @@ Dependencies and versions: hmmsearch: 3.1 - busco: 5.4.4 + busco: 5.5.0 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/summary.png Binary file test-data/proteome_results/summary.png has changed diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/full_table --- a/test-data/transcriptome_results/full_table Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/transcriptome_results/full_table Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) # Busco id Status Sequence Score Length OrthoDB url Description 774at6656 Missing diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/missing_buscos_list --- a/test-data/transcriptome_results/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/transcriptome_results/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/short_summary --- a/test-data/transcriptome_results/short_summary Fri Apr 14 08:13:46 2023 +0000 +++ b/test-data/transcriptome_results/short_summary Tue Nov 14 13:03:37 2023 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.4.4 +# BUSCO version is: 5.5.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_12.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/4/3/b/dataset_43bb7c5f-29dc-4638-a19d-abb98c145794.dat # BUSCO was run in mode: euk_tran ***** Results: ***** @@ -16,4 +16,4 @@ Dependencies and versions: hmmsearch: 3.1 metaeuk: 6.a5d39d9 - busco: 5.4.4 + busco: 5.5.0 diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/summary.png Binary file test-data/transcriptome_results/summary.png has changed