Mercurial > repos > iuc > busco
changeset 19:2a5b8b9936bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
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--- 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 $outputs: && mkdir BUSCO_summaries @@ -78,6 +86,7 @@ cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true #end if + ]]> </command> <inputs> <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." /> @@ -102,6 +111,7 @@ <option value="prot">annotated gene sets (protein)</option> </param> <when value="geno"> + <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/> <conditional name="use_augustus"> <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk"> <option value="yes">Yes, use Augustus</option> @@ -162,8 +172,10 @@ <section name="adv" title="Advanced Options" expanded="False"> <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> + <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/> </section> </inputs> + <outputs> <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> <filter>outputs and 'short_summary' in outputs</filter> @@ -178,7 +190,11 @@ <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff"> <filter>outputs and 'gff' in outputs</filter> </data> + <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff"> + <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter> + </data> </outputs> + <tests> <test expect_num_outputs="4"> <param name="input" value="genome.fa" /> @@ -244,7 +260,7 @@ <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"> + <test expect_num_outputs="4"> <param name="input" value="genome.fa" /> <conditional name="lineage"> <param name="lineage_mode" value="select_lineage" /> @@ -252,6 +268,7 @@ </conditional> <conditional name="busco_mode"> <param name="mode" value="geno" /> + <param name="miniprot" value="true"/> <conditional name="use_augustus"> <param name="use_augustus_selector" value="yes" /> <conditional name="aug_prediction"> @@ -269,6 +286,8 @@ <has_text text="##gff-version 3" /> </assert_contents> </output> + <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. --> + <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/> </test> <test expect_num_outputs="3"> <param name="input" value="genome.fa" />
--- 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 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">5.4.6</token> + <token name="@TOOL_VERSION@">5.5.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="citations">
--- 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
--- 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
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--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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