| Previous changeset 8:602fb8e63aa7 (2020-12-30) Next changeset 10:2dd755c1c6ff (2021-07-15) |
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Commit message:
"planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" |
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modified:
busco.xml macros.xml test-data/genome_results/full_table test-data/genome_results/missing_buscos_list test-data/genome_results/short_summary test-data/proteome_results/full_table test-data/proteome_results/missing_buscos_list test-data/proteome_results/short_summary test-data/transcriptome_results/full_table test-data/transcriptome_results/missing_buscos_list test-data/transcriptome_results/short_summary |
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added:
test-data/genome_results_metaeuk/full_table test-data/genome_results_metaeuk/missing_buscos_list test-data/genome_results_metaeuk/short_summary test-data/genome_results_metaeuk/summary.png test-data/proteome_results/summary.png test-data/transcriptome_results/summary.png |
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| diff -r 602fb8e63aa7 -r cf13a1e03e5b busco.xml --- a/busco.xml Wed Dec 30 14:07:37 2020 +0000 +++ b/busco.xml Mon Mar 15 21:27:17 2021 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@">\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 <macros>\n <import>macros.xml</import>\n@@ -6,129 +6,262 @@\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">busco</requirement>\n <requirement type="package" version="1.32">tar</requirement>\n+ <requirement type="package" version="1">fonts-conda-ecosystem</requirement>\n </requirements>\n+ <version_command>busco --version</version_command>\n <command><![CDATA[\n if [ -z "\\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\\$(dirname \\$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\\$(realpath \\${BUSCO_PATH}/../config) ; fi &&\n cp -r "\\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&\n export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&\n \n-#if $adv.aug_prediction.augustus_mode == \'history\':\n+#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\' and $busco_mode.use_augustus.aug_prediction.augustus_mode == \'history\':\n ## Using an augustus model from history, we need to unzip it and let augustus find it\n mkdir -p \'augustus_dir/species/\' &&\n- tar -C \'augustus_dir/species/\' -xzf \'${adv.aug_prediction.augustus_model}\' &&\n+ tar -C \'augustus_dir/species/\' -xzf \'${busco_mode.use_augustus.aug_prediction.augustus_model}\' &&\n #end if\n \n busco\n --in \'${input}\'\n --lineage_dataset \'${lineage_dataset}\'\n --update-data\n---mode \'${mode}\'\n--o busco_galaxy\n+--mode \'${busco_mode.mode}\'\n+--out busco_galaxy\n --cpu \\${GALAXY_SLOTS:-4}\n --evalue ${adv.evalue}\n-${adv.long}\n --limit ${adv.limit}\n-#if $adv.aug_prediction.augustus_mode == \'builtin\':\n- --augustus_species \'${adv.aug_prediction.augustus_species}\'\n-#else if $adv.aug_prediction.augustus_mode == \'history\':\n- --augustus_species local\n+\n+#if $adv.auto_lineage:\n+ $adv.auto_lineage\n+#end if\n+#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\':\n+\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+ --augustus_species local\n+ #end if\n+#end if\n+\n+#if $adv.outputs and \'image\' in $adv.outputs:\n+ &&\n+ mkdir BUSCO_summaries\n+ &&\n+ ls -l busco_galaxy/run_*/ &&\n+ cp busco_galaxy/short_summary.*.txt BUSCO_summaries/\n+ &&\n+ generate_plot.py -wd BUSCO_summaries -rt specific\n #end if\n- ]]></command>\n \n+]]> </command>\n <inputs>\n- <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />\n- <param argument="--mode" type="select" label="Mode">\n- <option value="geno">Genome</option>\n- <option value="tran">Transcriptome</option>\n- <option value="prot">Proteome</option>\n- </param>\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="busco_mode">\n+ <param argument="--mode" type="select" label="Mode">\n+ <option value="geno">Genome assemblies (DNA)</option>\n+ <option value="tran">Transcriptome assemblies (DNA)</option>\n+ <option value="prot">annotated gene sets (protein)</option>\n+ </param>\n+ <when value="geno">\n+ <conditional name="use_augustus">\n+ <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">\n+ <option value="yes">Yes, use Augustus</option>\n+ <optio'..b'enome_results/missing_buscos_list" compare="diff" lines_diff="4"/>\n+ <test expect_num_outputs="3">\n+ <param name="input" value="genome.fa" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n+ <conditional name="busco_mode">\n+ <param name="mode" value="geno" />\n+ <conditional name="use_augustus">\n+ <param name="use_augustus_selector" value="yes" />\n+ <conditional name="aug_prediction">\n+ <param name="augustus_mode" value="history" />\n+ <param name="augustus_model" value="local.tar.gz" ftype="augustus" />\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <section name="adv">\n+ <param name="outputs" value="short_summary,missing" />\n+ </section>\n+ <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />\n+ <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />\n+ <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />\n+ </test>\n+ <test expect_num_outputs="4">\n+ <param name="input" value="genome.fa" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n+ <conditional name="busco_mode">\n+ <param name="mode" value="geno" />\n+ <conditional name="use_augustus">\n+ <param name="use_augustus_selector" value="no" />\n+ </conditional>\n+ </conditional>\n+ <section name="adv">\n+ <param name="outputs" value="short_summary,missing,image" />\n+ </section>\n+ <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="4" />\n+ <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="4" />\n+ <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="4" />\n+ <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />\n </test>\n </tests>\n- <help>\n+ <help><![CDATA[\n+\n+\n BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs\n+--------------------------------------------------------------------------------------------------------------\n+\n+Interpreting the results\n+^^^^^^^^^^^^^^^^^^^^^^^^\n+\n+BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a\n+genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete\n+and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.\n+\n+BUSCO completeness results make sense only in the context of the biology of your organism.\n+You have to understand whether missing or duplicated genes are of biological or technical origin.\n+For instance, a high level of duplication may be explained by a recent whole duplication event\n+(biological) or a chimeric assembly of haplotypes (technical).\n+Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.\n+Therefore you should filter them before a BUSCO analysis.\n+Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment\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+.\n \n .. _BUSCO: http://busco.ezlab.org/\n- </help>\n- <expand macro="citations"/>\n+\n+ ]]> </help>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 602fb8e63aa7 -r cf13a1e03e5b macros.xml --- a/macros.xml Wed Dec 30 14:07:37 2020 +0000 +++ b/macros.xml Mon Mar 15 21:27:17 2021 +0000 |
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| @@ -1,6 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">4.1.4</token> + <token name="@TOOL_VERSION@">5.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="citations"> <citations> |
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| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results/full_table --- a/test-data/genome_results/full_table Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/genome_results/full_table Mon Mar 15 21:27:17 2021 +0000 |
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| @@ -1,6 +1,6 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) -# Busco id Status Sequence Gene Start Gene End Score Length OrthoDB url Description +# Busco id Status Sequence Gene Start Gene End Strand Score Length OrthoDB url Description 774at6656 Missing 980at6656 Missing 997at6656 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 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing |
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| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results/missing_buscos_list --- a/test-data/genome_results/missing_buscos_list Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/genome_results/missing_buscos_list Mon Mar 15 21:27:17 2021 +0000 |
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| @@ -1,4 +1,4 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) # Busco id 100070at6656 |
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| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results/short_summary --- a/test-data/genome_results/short_summary Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/genome_results/short_summary Mon Mar 15 21:27:17 2021 +0000 |
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| @@ -1,7 +1,8 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmp0yshlkbl/files/d/c/0/dataset_dc06dd53-8ed0-477c-b8bd-dd9fe68fd7e0.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmp7tgu744e/files/3/3/6/dataset_336adf79-955a-4ca8-aeda-96fc1fce9a4c.dat # BUSCO was run in mode: genome +# Gene predictor used: augustus ***** Results: ***** |
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| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk/full_table Mon Mar 15 21:27:17 2021 +0000 |
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| b'@@ -0,0 +1,1016 @@\n+# BUSCO version is: 5.0.0 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)\n+# Busco id\tStatus\tSequence\tGene Start\tGene End\tStrand\tScore\tLength\tOrthoDB url\tDescription\n+774at6656\tMissing\n+980at6656\tMissing\n+997at6656\tMissing\n+1166at6656\tMissing\n+1885at6656\tMissing\n+1990at6656\tMissing\n+2148at6656\tMissing\n+2456at6656\tMissing\n+2473at6656\tMissing\n+3310at6656\tMissing\n+3585at6656\tMissing\n+3644at6656\tMissing\n+4136at6656\tMissing\n+4227at6656\tMissing\n+4864at6656\tMissing\n+5277at6656\tMissing\n+5616at6656\tMissing\n+6453at6656\tMissing\n+6563at6656\tMissing\n+6715at6656\tMissing\n+6820at6656\tMissing\n+7210at6656\tMissing\n+8145at6656\tMissing\n+8495at6656\tMissing\n+8847at6656\tMissing\n+8913at6656\tMissing\n+9647at6656\tMissing\n+9648at6656\tMissing\n+10240at6656\tMissing\n+10573at6656\tMissing\n+11384at6656\tMissing\n+12029at6656\tMissing\n+12174at6656\tMissing\n+12383at6656\tMissing\n+12771at6656\tMissing\n+12846at6656\tMissing\n+13019at6656\tMissing\n+13051at6656\tMissing\n+13736at6656\tMissing\n+13833at6656\tMissing\n+13858at6656\tMissing\n+13890at6656\tMissing\n+13934at6656\tMissing\n+14090at6656\tMissing\n+14257at6656\tMissing\n+14447at6656\tMissing\n+14995at6656\tMissing\n+15200at6656\tMissing\n+15697at6656\tMissing\n+15905at6656\tMissing\n+16061at6656\tMissing\n+16084at6656\tMissing\n+16220at6656\tMissing\n+16630at6656\tMissing\n+16648at6656\tMissing\n+17096at6656\tMissing\n+17122at6656\tMissing\n+17128at6656\tMissing\n+17748at6656\tMissing\n+18036at6656\tMissing\n+18055at6656\tMissing\n+18073at6656\tMissing\n+18630at6656\tMissing\n+18929at6656\tMissing\n+19044at6656\tMissing\n+19058at6656\tMissing\n+19104at6656\tMissing\n+19129at6656\tMissing\n+19208at6656\tMissing\n+19289at6656\tMissing\n+19590at6656\tMissing\n+19760at6656\tMissing\n+20093at6656\tMissing\n+20162at6656\tMissing\n+20267at6656\tMissing\n+20935at6656\tMissing\n+20936at6656\tMissing\n+21019at6656\tMissing\n+21191at6656\tMissing\n+21361at6656\tMissing\n+21367at6656\tMissing\n+21385at6656\tMissing\n+22098at6656\tMissing\n+22148at6656\tMissing\n+22358at6656\tMissing\n+22364at6656\tMissing\n+22468at6656\tMissing\n+22611at6656\tMissing\n+22887at6656\tMissing\n+23309at6656\tMissing\n+23388at6656\tMissing\n+23429at6656\tMissing\n+23917at6656\tMissing\n+24255at6656\tMissing\n+24427at6656\tMissing\n+24459at6656\tMissing\n+24556at6656\tMissing\n+24573at6656\tMissing\n+25554at6656\tMissing\n+25680at6656\tMissing\n+26078at6656\tMissing\n+26653at6656\tMissing\n+26734at6656\tMissing\n+27198at6656\tMissing\n+27515at6656\tMissing\n+27617at6656\tMissing\n+27655at6656\tMissing\n+28325at6656\tMissing\n+28380at6656\tMissing\n+28519at6656\tMissing\n+28685at6656\tMissing\n+28872at6656\tMissing\n+29213at6656\tMissing\n+29237at6656\tMissing\n+29365at6656\tMissing\n+29730at6656\tMissing\n+29744at6656\tMissing\n+30156at6656\tMissing\n+30184at6656\tMissing\n+30267at6656\tMissing\n+30463at6656\tMissing\n+30512at6656\tMissing\n+30526at6656\tMissing\n+30642at6656\tMissing\n+30822at6656\tMissing\n+30918at6656\tMissing\n+30962at6656\tMissing\n+31014at6656\tMissing\n+31119at6656\tMissing\n+31196at6656\tMissing\n+31333at6656\tMissing\n+31480at6656\tMissing\n+31615at6656\tMissing\n+31634at6656\tMissing\n+31820at6656\tMissing\n+31886at6656\tMissing\n+31919at6656\tMissing\n+32694at6656\tMissing\n+32733at6656\tMissing\n+32851at6656\tMissing\n+33187at6656\tMissing\n+33566at6656\tMissing\n+33794at6656\tMissing\n+34586at6656\tMissing\n+34917at6656\tMissing\n+35035at6656\tMissing\n+35548at6656\tMissing\n+35680at6656\tMissing\n+35708at6656\tMissing\n+35995at6656\tMissing\n+36374at6656\tMissing\n+36387at6656\tMissing\n+36403at6656\tMissing\n+36463at6656\tMissing\n+37030at6656\tMissing\n+37297at6656\tMissing\n+37387at6656\tMissing\n+37678at6656\tMissing\n+38140at6656\tMissing\n+38186at6656\tMissing\n+38303at6656\tMissing\n+38391at6656\tMissing\n+38567at6656\tMissing\n+38819at6656\tMissing\n+38928at6656\tMissing\n+39506at6656\tMissing\n+39548at6656\tMissing\n+39783at6656\tMissing\n+39809at6656\tMissing\n+39821at6656\tMissing\n+40065at6656\tMissing\n+40092at6656\tMissing\n+40213at6656\tMissing\n+40240at6656\tMissing\n+40319at6656\tMissing\n+40323at6656\tMissing\n+40399at6656\tMissing\n+40691at6656\tMissing\n+40929at6656\tMissing\n+41522at6656\t'..b'90at6656\tMissing\n+135702at6656\tMissing\n+135764at6656\tMissing\n+135828at6656\tMissing\n+135834at6656\tMissing\n+135859at6656\tMissing\n+135975at6656\tMissing\n+135994at6656\tMissing\n+136055at6656\tMissing\n+136095at6656\tMissing\n+136119at6656\tMissing\n+136224at6656\tMissing\n+136365at6656\tMissing\n+136559at6656\tMissing\n+136888at6656\tMissing\n+137050at6656\tMissing\n+137197at6656\tMissing\n+137202at6656\tMissing\n+137334at6656\tMissing\n+137338at6656\tMissing\n+137422at6656\tMissing\n+137609at6656\tMissing\n+137688at6656\tMissing\n+137709at6656\tMissing\n+137711at6656\tMissing\n+138243at6656\tMissing\n+138271at6656\tMissing\n+138379at6656\tMissing\n+138401at6656\tMissing\n+138502at6656\tMissing\n+138553at6656\tMissing\n+138659at6656\tMissing\n+138684at6656\tMissing\n+138937at6656\tMissing\n+139217at6656\tMissing\n+139553at6656\tMissing\n+139638at6656\tMissing\n+139744at6656\tMissing\n+139834at6656\tMissing\n+140076at6656\tMissing\n+140197at6656\tMissing\n+140198at6656\tMissing\n+140403at6656\tMissing\n+140461at6656\tMissing\n+140693at6656\tMissing\n+140874at6656\tMissing\n+140903at6656\tMissing\n+141031at6656\tMissing\n+141163at6656\tMissing\n+141166at6656\tMissing\n+141175at6656\tMissing\n+141298at6656\tMissing\n+141804at6656\tMissing\n+141859at6656\tMissing\n+141916at6656\tMissing\n+142388at6656\tMissing\n+142415at6656\tMissing\n+142522at6656\tMissing\n+142613at6656\tMissing\n+142661at6656\tMissing\n+142833at6656\tMissing\n+143154at6656\tMissing\n+143279at6656\tMissing\n+143459at6656\tMissing\n+143489at6656\tMissing\n+143562at6656\tMissing\n+143626at6656\tMissing\n+143709at6656\tMissing\n+143812at6656\tMissing\n+143930at6656\tMissing\n+144337at6656\tMissing\n+144652at6656\tMissing\n+144836at6656\tMissing\n+144851at6656\tMissing\n+144853at6656\tMissing\n+145033at6656\tMissing\n+145102at6656\tMissing\n+145443at6656\tMissing\n+145610at6656\tMissing\n+145811at6656\tMissing\n+145996at6656\tMissing\n+146007at6656\tMissing\n+146036at6656\tMissing\n+146087at6656\tMissing\n+146102at6656\tMissing\n+146103at6656\tMissing\n+146383at6656\tMissing\n+146600at6656\tMissing\n+146920at6656\tMissing\n+147002at6656\tMissing\n+147025at6656\tMissing\n+147322at6656\tMissing\n+147657at6656\tMissing\n+147723at6656\tMissing\n+147852at6656\tMissing\n+147891at6656\tMissing\n+147980at6656\tMissing\n+148134at6656\tMissing\n+148619at6656\tMissing\n+148713at6656\tMissing\n+148851at6656\tMissing\n+148890at6656\tMissing\n+149101at6656\tMissing\n+149126at6656\tMissing\n+149251at6656\tMissing\n+149405at6656\tMissing\n+149680at6656\tMissing\n+149753at6656\tMissing\n+149796at6656\tMissing\n+149819at6656\tMissing\n+149973at6656\tMissing\n+149977at6656\tMissing\n+150005at6656\tMissing\n+150049at6656\tMissing\n+150137at6656\tMissing\n+150182at6656\tMissing\n+150251at6656\tMissing\n+150327at6656\tMissing\n+150479at6656\tMissing\n+150583at6656\tMissing\n+150585at6656\tMissing\n+150667at6656\tMissing\n+150765at6656\tMissing\n+151102at6656\tMissing\n+151111at6656\tMissing\n+151114at6656\tMissing\n+151393at6656\tMissing\n+151436at6656\tMissing\n+151642at6656\tMissing\n+151658at6656\tMissing\n+152032at6656\tMissing\n+152109at6656\tMissing\n+152402at6656\tMissing\n+152534at6656\tMissing\n+152871at6656\tMissing\n+153155at6656\tMissing\n+153232at6656\tMissing\n+153312at6656\tMissing\n+153534at6656\tMissing\n+153693at6656\tMissing\n+153873at6656\tMissing\n+154133at6656\tMissing\n+154415at6656\tMissing\n+154507at6656\tMissing\n+155285at6656\tMissing\n+156057at6656\tMissing\n+156081at6656\tMissing\n+156111at6656\tMissing\n+156305at6656\tMissing\n+156395at6656\tMissing\n+156728at6656\tMissing\n+156824at6656\tMissing\n+156882at6656\tMissing\n+156975at6656\tMissing\n+157486at6656\tMissing\n+157579at6656\tMissing\n+157851at6656\tMissing\n+157879at6656\tMissing\n+158194at6656\tMissing\n+158760at6656\tMissing\n+159231at6656\tMissing\n+159420at6656\tMissing\n+159542at6656\tMissing\n+160675at6656\tMissing\n+160705at6656\tMissing\n+161435at6656\tMissing\n+162059at6656\tMissing\n+162147at6656\tMissing\n+162594at6656\tMissing\n+162628at6656\tMissing\n+162841at6656\tMissing\n+163670at6656\tMissing\n+163896at6656\tMissing\n+164354at6656\tMissing\n+164512at6656\tMissing\n+165142at6656\tMissing\n+165207at6656\tMissing\n+165493at6656\tMissing\n+166476at6656\tMissing\n+166479at6656\tMissing\n+166485at6656\tMissing\n+169220at6656\tMissing\n' 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| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk/missing_buscos_list Mon Mar 15 21:27:17 2021 +0000 |
| b |
| b'@@ -0,0 +1,1014 @@\n+# BUSCO version is: 5.0.0 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)\n+# Busco 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|
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk/short_summary Mon Mar 15 21:27:17 2021 +0000 |
| [ |
| @@ -0,0 +1,15 @@ +# BUSCO version is: 5.0.0 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmp7tgu744e/files/3/e/e/dataset_3ee78f14-2ccd-4666-af87-075e725e09bd.dat +# BUSCO was run in mode: genome +# Gene predictor used: metaeuk + + ***** 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) + 1013 Total BUSCO groups searched |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/summary.png |
| b |
| Binary file test-data/genome_results_metaeuk/summary.png has changed |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/full_table --- a/test-data/proteome_results/full_table Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/proteome_results/full_table Mon Mar 15 21:27:17 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) # Busco id Status Sequence Score Length OrthoDB url Description 774at6656 Missing |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/missing_buscos_list --- a/test-data/proteome_results/missing_buscos_list Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/proteome_results/missing_buscos_list Mon Mar 15 21:27:17 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) # Busco id 100070at6656 |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/short_summary --- a/test-data/proteome_results/short_summary Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/proteome_results/short_summary Mon Mar 15 21:27:17 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmp0yshlkbl/files/0/9/0/dataset_090e32f3-7f4a-47b2-b1c3-c80bb88da90f.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmp7tgu744e/files/8/e/0/dataset_8e0c0f40-2615-49a6-a2aa-9e5ad5f5a163.dat # BUSCO was run in mode: proteins ***** Results: ***** |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/summary.png |
| b |
| Binary file test-data/proteome_results/summary.png has changed |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/full_table --- a/test-data/transcriptome_results/full_table Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/transcriptome_results/full_table Mon Mar 15 21:27:17 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 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://www.orthodb.org/v10?query=22364at6656 importin-5 +22364at6656 Complete BUSCOaEOG7B0HST:0-2699 1355.6 788 https://www.orthodb.org/v10?query=22364at6656 importin-5 22468at6656 Missing 22611at6656 Missing 22887at6656 Missing |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/missing_buscos_list --- a/test-data/transcriptome_results/missing_buscos_list Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/transcriptome_results/missing_buscos_list Mon Mar 15 21:27:17 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) # Busco id 100070at6656 |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/short_summary --- a/test-data/transcriptome_results/short_summary Wed Dec 30 14:07:37 2020 +0000 +++ b/test-data/transcriptome_results/short_summary Mon Mar 15 21:27:17 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# BUSCO version is: 4.1.4 +# BUSCO version is: 5.0.0 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013) -# Summarized benchmarking in BUSCO notation for file /tmp/tmp0yshlkbl/files/c/d/5/dataset_cd590461-e7d2-4927-8b96-f3282e2da236.dat +# Summarized benchmarking in BUSCO notation for file /tmp/tmpn3gmbt1s/files/4/1/3/dataset_413f631e-7113-4502-9085-5f25549301e4.dat # BUSCO was run in mode: transcriptome ***** Results: ***** |
| b |
| diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/summary.png |
| b |
| Binary file test-data/transcriptome_results/summary.png has changed |
