| Previous changeset 19:2a5b8b9936bf (2023-11-14) Next changeset 21:2babe6d5c561 (2024-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 9bf18dbcef34a48d3c40150ee953706bececfdd1 |
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modified:
busco.xml test-data/genome_results/short_summary test-data/genome_results_metaeuk/short_summary test-data/genome_results_metaeuk_auto/out.gff test-data/proteome_results/short_summary test-data/transcriptome_results/short_summary |
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| diff -r 2a5b8b9936bf -r ea8146ee148f busco.xml --- a/busco.xml Tue Nov 14 13:03:37 2023 +0000 +++ b/busco.xml Mon Mar 18 16:01:49 2024 +0000 |
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| @@ -209,7 +209,7 @@ </conditional> </conditional> <param name="outputs" value="short_summary,missing,gff" /> - <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" /> + <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> <output name="busco_gff"> <assert_contents> @@ -233,7 +233,7 @@ <param name="mode" value="prot" /> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" /> + <output name="busco_sum" file="proteome_results/short_summary" compare="re_match_multiline" /> <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> @@ -254,7 +254,7 @@ <param name="mode" value="tran" /> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" /> + <output name="busco_sum" file="transcriptome_results/short_summary" compare="re_match_multiline" /> <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" /> @@ -278,7 +278,7 @@ </conditional> </conditional> <param name="outputs" value="short_summary,gff" /> - <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" /> + <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/> <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> <output name="busco_gff"> <assert_contents> @@ -306,7 +306,7 @@ </conditional> </conditional> <param name="outputs" value="short_summary,missing" /> - <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" /> + <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> </test> @@ -323,11 +323,15 @@ </conditional> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" /> + <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="re_match_multiline" /> <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> - <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" /> + <output name="busco_gff" ftype="gff3"> + <assert_contents> + <has_n_lines n="13"/> + </assert_contents> + </output> </test> <test expect_num_outputs="5"> <param name="input" value="genome.fa" /> @@ -343,7 +347,7 @@ </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" /> - <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" /> + <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" /> <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> <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" /> |
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| diff -r 2a5b8b9936bf -r ea8146ee148f test-data/genome_results/short_summary --- a/test-data/genome_results/short_summary Tue Nov 14 13:03:37 2023 +0000 +++ b/test-data/genome_results/short_summary Mon Mar 18 16:01:49 2024 +0000 |
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| @@ -1,35 +1,35 @@ -# 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/tmpbmq1q2c6/files/8/e/b/dataset_8eb218b1-f367-4315-9915-554c009808cb.dat +# BUSCO version is: 5\.5\.0 +# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) +# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ # BUSCO was run in mode: euk_genome_aug # Gene predictor used: augustus - ***** Results: ***** + \*\*\*\*\* Results: \*\*\*\*\* - C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 - 1 Complete BUSCOs (C) - 1 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 0 Fragmented BUSCOs (F) - 1012 Missing BUSCOs (M) + C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013 + 1 Complete BUSCOs \(C\) + 1 Complete and single-copy BUSCOs \(S\) + 0 Complete and duplicated BUSCOs \(D\) + 0 Fragmented BUSCOs \(F\) + 1012 Missing BUSCOs \(M\) 1013 Total BUSCO groups searched Assembly Statistics: 1 Number of scaffolds 1 Number of contigs 62370 Total length - 0.000% Percent gaps + 0\.000% Percent gaps 62 KB Scaffold N50 62 KB Contigs N50 Dependencies and versions: - hmmsearch: 3.1 - bbtools: 39.01 - makeblastdb: 2.14.0+ - tblastn: 2.14.0+ - augustus: 3.5.0 - gff2gbSmallDNA.pl: None - new_species.pl: None + hmmsearch: [0-9\.\+]+ + bbtools: [0-9\.\+]+ + makeblastdb: [0-9\.\+]+ + tblastn: [0-9\.\+]+ + augustus: [0-9\.\+]+ + gff2gbSmallDNA\.pl: None + new_species\.pl: None etraining: None - busco: 5.5.0 + busco: [0-9\.\+]+ |
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| diff -r 2a5b8b9936bf -r ea8146ee148f test-data/genome_results_metaeuk/short_summary --- a/test-data/genome_results_metaeuk/short_summary Tue Nov 14 13:03:37 2023 +0000 +++ b/test-data/genome_results_metaeuk/short_summary Mon Mar 18 16:01:49 2024 +0000 |
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| @@ -1,30 +1,30 @@ -# 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/tmp5_syjrgy/files/1/d/2/dataset_1d20a949-adce-4511-8cab-345d59a61a05.dat +# BUSCO version is: 5\.5\.0 +# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) +# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ # BUSCO was run in mode: euk_genome_met # Gene predictor used: metaeuk - ***** Results: ***** + \*\*\*\*\* Results: \*\*\*\*\* - C:0.2%[S:0.2%,D:0.0%],F:0.0%,M:99.8%,n:1013 - 2 Complete BUSCOs (C) - 2 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 0 Fragmented BUSCOs (F) - 1011 Missing BUSCOs (M) + C:0\.2%\[S:0\.2%,D:0\.0%\],F:0\.0%,M:99\.8%,n:1013 + 2 Complete BUSCOs \(C\) + 2 Complete and single-copy BUSCOs \(S\) + 0 Complete and duplicated BUSCOs \(D\) + 0 Fragmented BUSCOs \(F\) + 1011 Missing BUSCOs \(M\) 1013 Total BUSCO groups searched Assembly Statistics: 1 Number of scaffolds 1 Number of contigs 62370 Total length - 0.000% Percent gaps + 0\.000% Percent gaps 62 KB Scaffold N50 62 KB Contigs N50 Dependencies and versions: - hmmsearch: 3.1 - bbtools: 39.01 - metaeuk: 6.a5d39d9 - busco: 5.5.0 + hmmsearch: [0-9\.\+]+ + bbtools: [0-9\.\+]+ + metaeuk: [0-9a-z\.\+]+ + busco: [0-9\.\+]+ |
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| diff -r 2a5b8b9936bf -r ea8146ee148f test-data/genome_results_metaeuk_auto/out.gff --- a/test-data/genome_results_metaeuk_auto/out.gff Tue Nov 14 13:03:37 2023 +0000 +++ b/test-data/genome_results_metaeuk_auto/out.gff Mon Mar 18 16:01:49 2024 +0000 |
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| @@ -1,5 +1,5 @@ ##gff-version 3 -sample MetaEuk gene 34846 35679 545 - . Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845 -sample MetaEuk mRNA 34846 35679 545 - . Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845_mRNA;Parent=1053181at2759_7227_0:001f92|sample|-|34845 -sample MetaEuk exon 34846 35679 545 - . Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845_exon_0;Parent=1053181at2759_7227_0:001f92|sample|-|34845_mRNA -sample MetaEuk CDS 34846 35679 545 - . Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845_CDS_0;Parent=1053181at2759_7227_0:001f92|sample|-|34845_exon_0 +sample MetaEuk gene 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845 +sample MetaEuk mRNA 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_mRNA;Parent=1053181at2759_7245_0:00200b|sample|-|34845 +sample MetaEuk exon 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_exon_0;Parent=1053181at2759_7245_0:00200b|sample|-|34845_mRNA +sample MetaEuk CDS 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_CDS_0;Parent=1053181at2759_7245_0:00200b|sample|-|34845_exon_0 |
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| diff -r 2a5b8b9936bf -r ea8146ee148f test-data/proteome_results/short_summary --- a/test-data/proteome_results/short_summary Tue Nov 14 13:03:37 2023 +0000 +++ b/test-data/proteome_results/short_summary Mon Mar 18 16:01:49 2024 +0000 |
| [ |
| @@ -1,18 +1,18 @@ -# 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/tmp5_syjrgy/files/b/a/7/dataset_ba764d57-9365-4d54-a1f8-ac1350df0747.dat +# BUSCO version is: 5\.5\.0 +# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) +# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ # BUSCO was run in mode: proteins - ***** Results: ***** + \*\*\*\*\* Results: \*\*\*\*\* - C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 - 1 Complete BUSCOs (C) - 1 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 0 Fragmented BUSCOs (F) - 1012 Missing BUSCOs (M) + C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013 + 1 Complete BUSCOs \(C\) + 1 Complete and single-copy BUSCOs \(S\) + 0 Complete and duplicated BUSCOs \(D\) + 0 Fragmented BUSCOs \(F\) + 1012 Missing BUSCOs \(M\) 1013 Total BUSCO groups searched Dependencies and versions: - hmmsearch: 3.1 - busco: 5.5.0 + hmmsearch: [0-9\.\+]+ + busco: [0-9\.\+]+ |
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| diff -r 2a5b8b9936bf -r ea8146ee148f test-data/transcriptome_results/short_summary --- a/test-data/transcriptome_results/short_summary Tue Nov 14 13:03:37 2023 +0000 +++ b/test-data/transcriptome_results/short_summary Mon Mar 18 16:01:49 2024 +0000 |
| [ |
| @@ -1,19 +1,19 @@ -# 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/tmp5_syjrgy/files/4/3/b/dataset_43bb7c5f-29dc-4638-a19d-abb98c145794.dat +# BUSCO version is: 5\.5\.0 +# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) +# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ # BUSCO was run in mode: euk_tran - ***** Results: ***** + \*\*\*\*\* Results: \*\*\*\*\* - C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 - 1 Complete BUSCOs (C) - 1 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 0 Fragmented BUSCOs (F) - 1012 Missing BUSCOs (M) + C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013 + 1 Complete BUSCOs \(C\) + 1 Complete and single-copy BUSCOs \(S\) + 0 Complete and duplicated BUSCOs \(D\) + 0 Fragmented BUSCOs \(F\) + 1012 Missing BUSCOs \(M\) 1013 Total BUSCO groups searched Dependencies and versions: - hmmsearch: 3.1 - metaeuk: 6.a5d39d9 - busco: 5.5.0 + hmmsearch: [0-9\.\+]+ + metaeuk: [0-9a-z\.\+]+ + busco: [0-9\.\+]+ |