| Previous changeset 11:0d243f458b53 (2021-07-26) Next changeset 13:46ae58b1d792 (2021-11-05) |
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Commit message:
"planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" |
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modified:
busco.xml macros.xml |
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added:
test-data/genome_results_metaeuk_auto/full_table test-data/genome_results_metaeuk_auto/missing_buscos_list test-data/genome_results_metaeuk_auto/short_summary test-data/genome_results_metaeuk_auto/summary.png |
| b |
| diff -r 0d243f458b53 -r 1278204240d8 busco.xml --- a/busco.xml Mon Jul 26 21:29:40 2021 +0000 +++ b/busco.xml Tue Nov 02 09:40:29 2021 +0000 |
| [ |
| b'@@ -1,5 +1,8 @@\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+ <xrefs>\n+ <xref type="bio.tools">busco</xref>\n+ </xrefs>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -22,7 +25,6 @@\n \n busco\n --in \'${input}\'\n---lineage_dataset \'${lineage_dataset}\'\n --update-data\n --mode \'${busco_mode.mode}\'\n --out busco_galaxy\n@@ -30,8 +32,10 @@\n --evalue ${adv.evalue}\n --limit ${adv.limit}\n \n-#if $adv.auto_lineage:\n- $adv.auto_lineage\n+#if $lineage.lineage_mode == "auto_detect":\n+ $lineage.auto_lineage\n+#else if $lineage.lineage_mode == "select_lineage":\n+ --lineage_dataset \'${lineage.lineage_dataset}\'\n #end if\n #if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\':\n \n@@ -96,18 +100,28 @@\n <when value="prot" />\n </conditional>\n \n- <param argument="--lineage_dataset" type="select" label="Lineage">\n- <expand macro="lineages" />\n- </param>\n+ <conditional name="lineage">\n+ <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">\n+ <option value="auto_detect">Auto-detect</option>\n+ <option value="select_lineage">Select lineage</option>\n+ </param>\n+ <when value="auto_detect">\n+ <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">\n+ <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>\n+ <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>\n+ <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>\n+ </param>\n+ </when>\n+ <when value="select_lineage">\n+ <param argument="--lineage_dataset" type="select" label="Lineage">\n+ <expand macro="lineages" />\n+ </param>\n+ </when>\n+ </conditional>\n \n <section name="adv" title="Advanced Options" expanded="False">\n <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />\n <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />\n- <param name="auto_lineage" type="select" optional="true" label="Run auto-lineage to find optimal lineage path">\n- <option value="--auto-lineage">Run auto-lineage to find optimum lineage path</option>\n- <option value="--auto-lineage-prok">Run auto-lineage just on non-eukaryote trees to find optimum lineage path</option>\n- <option value="--auto-lineage-euk">Run auto-placement just on eukaryote tree to find optimum lineage path</option>\n- </param>\n <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">\n <option value="short_summary">short summary text</option>\n <option value="missing">list with missing IDs</option>\n@@ -130,7 +144,10 @@\n <tests>\n <test expect_num_outputs="3">\n <param name="input" value="genome.fa" />\n- <param name="lineage_dataset" value="arthropoda_odb10" />\n+ <conditional name="lineage">\n+ <param name="lineage_mode" value="select_lineage" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n+ </conditional>\n <conditional name="busco_mode">\n <param name="mode" value="geno" />\n <conditional name="use_augustus">\n@@ -150,7 +167,10 @@\n </test>\n <test expect_num_outputs="4">\n <param '..b'ut name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />\n </test>\n <test expect_num_outputs="2">\n <param name="input" value="genome.fa" />\n- <param name="lineage_dataset" value="arthropoda_odb10" />\n+ <conditional name="lineage">\n+ <param name="lineage_mode" value="select_lineage" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n+ </conditional>\n <conditional name="busco_mode">\n <param name="mode" value="geno" />\n <conditional name="use_augustus">\n@@ -198,7 +223,10 @@\n </test>\n <test expect_num_outputs="3">\n <param name="input" value="genome.fa" />\n- <param name="lineage_dataset" value="arthropoda_odb10" />\n+ <conditional name="lineage">\n+ <param name="lineage_mode" value="select_lineage" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n+ </conditional>\n <conditional name="busco_mode">\n <param name="mode" value="geno" />\n <conditional name="use_augustus">\n@@ -218,7 +246,10 @@\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="lineage">\n+ <param name="lineage_mode" value="select_lineage" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n+ </conditional>\n <conditional name="busco_mode">\n <param name="mode" value="geno" />\n <conditional name="use_augustus">\n@@ -228,11 +259,31 @@\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="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />\n+ <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />\n+ <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />\n <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />\n </test>\n+ <test expect_num_outputs="4">\n+ <param name="input" value="genome.fa" />\n+ <conditional name="lineage">\n+ <param name="lineage_mode" value="auto_detect" />\n+ <param name="auto_lineage" value="--auto-lineage" />\n+ </conditional>\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_auto/short_summary" compare="diff" lines_diff="4" />\n+ <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="0" />\n+ <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="0" />\n+ <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r 0d243f458b53 -r 1278204240d8 macros.xml --- a/macros.xml Mon Jul 26 21:29:40 2021 +0000 +++ b/macros.xml Tue Nov 02 09:40:29 2021 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">5.2.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="citations"> <citations> |
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| diff -r 0d243f458b53 -r 1278204240d8 test-data/genome_results_metaeuk_auto/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk_auto/full_table Tue Nov 02 09:40:29 2021 +0000 |
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| @@ -0,0 +1,258 @@ +# BUSCO version is: 5.2.2 +# 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 +83779at2759 Missing +87842at2759 Missing +97116at2759 Missing +100698at2759 Missing +142542at2759 Missing +156083at2759 Missing +160593at2759 Missing +166920at2759 Missing +176625at2759 Missing +179362at2759 Missing +245208at2759 Missing +257318at2759 Missing +261328at2759 Missing +261419at2759 Missing +270107at2759 Missing +271586at2759 Missing +290630at2759 Missing +293315at2759 Missing +296129at2759 Missing +299766at2759 Missing +306227at2759 Missing +320059at2759 Missing +324863at2759 Missing +325552at2759 Missing +330169at2759 Missing +331411at2759 Missing +341721at2759 Missing +345441at2759 Missing +355408at2759 Missing +369837at2759 Missing +375960at2759 Missing +383503at2759 Missing +388820at2759 Missing +390348at2759 Missing +392369at2759 Missing +396755at2759 Missing +418107at2759 Missing +426305at2759 Missing +450058at2759 Missing +453044at2759 Missing +457861at2759 Missing +464990at2759 Missing +491869at2759 Missing +513979at2759 Missing +543764at2759 Missing +549762at2759 Missing +551907at2759 Missing +570797at2759 Missing +582756at2759 Missing +598949at2759 Missing +604979at2759 Missing +621827at2759 Missing +625387at2759 Missing +655400at2759 Missing +664730at2759 Missing +671536at2759 Missing +671846at2759 Missing +673132at2759 Missing +674160at2759 Missing +674169at2759 Missing +679187at2759 Missing +679771at2759 Missing +687505at2759 Missing +692986at2759 Missing +708105at2759 Missing +719531at2759 Missing +720340at2759 Missing +721605at2759 Missing +722805at2759 Missing +734341at2759 Missing +734666at2759 Missing +736068at2759 Missing +751335at2759 Missing +759498at2759 Missing +761109at2759 Missing +768809at2759 Missing +774318at2759 Missing +777920at2759 Missing +779909at2759 Missing +801857at2759 Missing +814241at2759 Missing +817008at2759 Missing +834694at2759 Missing +836599at2759 Missing +844748at2759 Missing +855834at2759 Missing +858842at2759 Missing +865202at2759 Missing +866359at2759 Missing +869548at2759 Missing +878143at2759 Missing +887370at2759 Missing +891751at2759 Missing +898782at2759 Missing +901894at2759 Missing +905026at2759 Missing +911863at2759 Missing +917326at2759 Missing +918816at2759 Missing +919955at2759 Missing +923657at2759 Missing +924753at2759 Missing +931188at2759 Missing +937275at2759 Missing +937686at2759 Missing +939345at2759 Missing +944899at2759 Missing +946128at2759 Missing +956854at2759 Missing +973442at2759 Missing +974865at2759 Missing +975158at2759 Missing +975557at2759 Missing +976469at2759 Missing +981902at2759 Missing +996662at2759 Missing +1001705at2759 Missing +1003258at2759 Missing +1010730at2759 Missing +1014314at2759 Missing +1018517at2759 Missing +1019762at2759 Missing +1025450at2759 Missing +1030907at2759 Missing +1032689at2759 Missing +1038775at2759 Missing +1041560at2759 Missing +1049599at2759 Missing +1051021at2759 Missing +1053181at2759 Complete sample 34845 35678 - 45.0 149 +1057950at2759 Missing +1065019at2759 Missing +1076134at2759 Missing +1079130at2759 Missing +1079827at2759 Missing +1085752at2759 Missing +1087488at2759 Missing +1090038at2759 Missing +1094121at2759 Missing +1096688at2759 Missing +1106766at2759 Missing +1107630at2759 Missing +1108845at2759 Missing +1111142at2759 Missing +1112002at2759 Missing +1115196at2759 Missing +1128607at2759 Missing +1129824at2759 Missing +1138059at2759 Missing +1157302at2759 Missing +1161199at2759 Missing +1173229at2759 Missing +1178688at2759 Missing +1182451at2759 Missing +1193442at2759 Missing +1194691at2759 Missing +1194797at2759 Missing +1197019at2759 Missing +1200489at2759 Missing +1217666at2759 Missing +1220881at2759 Missing +1222562at2759 Missing +1223488at2759 Missing +1228942at2759 Missing +1233814at2759 Missing +1236198at2759 Missing +1247641at2759 Missing +1248958at2759 Missing +1249159at2759 Missing +1251252at2759 Missing +1257440at2759 Missing +1258856at2759 Missing +1259741at2759 Missing +1260807at2759 Missing +1264469at2759 Missing +1266231at2759 Missing +1269244at2759 Missing +1269649at2759 Missing +1275837at2759 Missing +1284731at2759 Missing +1287094at2759 Missing +1287401at2759 Missing +1291729at2759 Missing +1304061at2759 Missing +1309031at2759 Missing +1312453at2759 Missing +1314980at2759 Missing +1322299at2759 Missing +1322642at2759 Missing +1323575at2759 Missing +1324510at2759 Missing +1338131at2759 Missing +1339553at2759 Missing +1342242at2759 Missing +1346165at2759 Missing +1346432at2759 Missing +1348942at2759 Missing +1355894at2759 Missing +1358374at2759 Missing +1364586at2759 Missing +1370285at2759 Missing +1370304at2759 Missing +1377237at2759 Missing +1379600at2759 Missing +1380409at2759 Missing +1382842at2759 Missing +1395649at2759 Missing +1398309at2759 Missing +1404162at2759 Missing +1405073at2759 Missing +1405146at2759 Missing +1407446at2759 Missing +1421503at2759 Missing +1423847at2759 Missing +1426075at2759 Missing +1428265at2759 Missing +1428854at2759 Missing +1430056at2759 Missing +1432328at2759 Missing +1434266at2759 Missing +1440961at2759 Missing +1441854at2759 Missing +1442062at2759 Missing +1445102at2759 Missing +1450538at2759 Missing +1454155at2759 Missing +1455730at2759 Missing +1459797at2759 Missing +1474000at2759 Missing +1479417at2759 Missing +1488235at2759 Missing +1488436at2759 Missing +1490022at2759 Missing +1504863at2759 Missing +1513531at2759 Missing +1525971at2759 Missing +1526152at2759 Missing +1530008at2759 Missing +1538526at2759 Missing +1545004at2759 Missing +1552706at2759 Missing +1558822at2759 Missing +1563319at2759 Missing +1567796at2759 Missing +1575179at2759 Missing +1576404at2759 Missing +1588798at2759 Missing +1593937at2759 Missing +1617752at2759 Missing +1620056at2759 Missing +1623701at2759 Missing +1626636at2759 Missing +1633672at2759 Missing +1645187at2759 Missing |
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| diff -r 0d243f458b53 -r 1278204240d8 test-data/genome_results_metaeuk_auto/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk_auto/missing_buscos_list Tue Nov 02 09:40:29 2021 +0000 |
| b |
| @@ -0,0 +1,257 @@ +# BUSCO version is: 5.2.2 +# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) +# Busco id +1001705at2759 +1003258at2759 +100698at2759 +1010730at2759 +1014314at2759 +1018517at2759 +1019762at2759 +1025450at2759 +1030907at2759 +1032689at2759 +1038775at2759 +1041560at2759 +1049599at2759 +1051021at2759 +1057950at2759 +1065019at2759 +1076134at2759 +1079130at2759 +1079827at2759 +1085752at2759 +1087488at2759 +1090038at2759 +1094121at2759 +1096688at2759 +1106766at2759 +1107630at2759 +1108845at2759 +1111142at2759 +1112002at2759 +1115196at2759 +1128607at2759 +1129824at2759 +1138059at2759 +1157302at2759 +1161199at2759 +1173229at2759 +1178688at2759 +1182451at2759 +1193442at2759 +1194691at2759 +1194797at2759 +1197019at2759 +1200489at2759 +1217666at2759 +1220881at2759 +1222562at2759 +1223488at2759 +1228942at2759 +1233814at2759 +1236198at2759 +1247641at2759 +1248958at2759 +1249159at2759 +1251252at2759 +1257440at2759 +1258856at2759 +1259741at2759 +1260807at2759 +1264469at2759 +1266231at2759 +1269244at2759 +1269649at2759 +1275837at2759 +1284731at2759 +1287094at2759 +1287401at2759 +1291729at2759 +1304061at2759 +1309031at2759 +1312453at2759 +1314980at2759 +1322299at2759 +1322642at2759 +1323575at2759 +1324510at2759 +1338131at2759 +1339553at2759 +1342242at2759 +1346165at2759 +1346432at2759 +1348942at2759 +1355894at2759 +1358374at2759 +1364586at2759 +1370285at2759 +1370304at2759 +1377237at2759 +1379600at2759 +1380409at2759 +1382842at2759 +1395649at2759 +1398309at2759 +1404162at2759 +1405073at2759 +1405146at2759 +1407446at2759 +1421503at2759 +1423847at2759 +142542at2759 +1426075at2759 +1428265at2759 +1428854at2759 +1430056at2759 +1432328at2759 +1434266at2759 +1440961at2759 +1441854at2759 +1442062at2759 +1445102at2759 +1450538at2759 +1454155at2759 +1455730at2759 +1459797at2759 +1474000at2759 +1479417at2759 +1488235at2759 +1488436at2759 +1490022at2759 +1504863at2759 +1513531at2759 +1525971at2759 +1526152at2759 +1530008at2759 +1538526at2759 +1545004at2759 +1552706at2759 +1558822at2759 +156083at2759 +1563319at2759 +1567796at2759 +1575179at2759 +1576404at2759 +1588798at2759 +1593937at2759 +160593at2759 +1617752at2759 +1620056at2759 +1623701at2759 +1626636at2759 +1633672at2759 +1645187at2759 +166920at2759 +176625at2759 +179362at2759 +245208at2759 +257318at2759 +261328at2759 +261419at2759 +270107at2759 +271586at2759 +290630at2759 +293315at2759 +296129at2759 +299766at2759 +306227at2759 +320059at2759 +324863at2759 +325552at2759 +330169at2759 +331411at2759 +341721at2759 +345441at2759 +355408at2759 +369837at2759 +375960at2759 +383503at2759 +388820at2759 +390348at2759 +392369at2759 +39650at2759 +396755at2759 +418107at2759 +426305at2759 +450058at2759 +453044at2759 +457861at2759 +464990at2759 +491869at2759 +513979at2759 +543764at2759 +549762at2759 +551907at2759 +570797at2759 +582756at2759 +598949at2759 +604979at2759 +621827at2759 +625387at2759 +655400at2759 +664730at2759 +671536at2759 +671846at2759 +673132at2759 +674160at2759 +674169at2759 +679187at2759 +679771at2759 +687505at2759 +692986at2759 +708105at2759 +719531at2759 +720340at2759 +721605at2759 +722805at2759 +734341at2759 +734666at2759 +736068at2759 +751335at2759 +759498at2759 +761109at2759 +768809at2759 +774318at2759 +777920at2759 +779909at2759 +801857at2759 +814241at2759 +817008at2759 +834694at2759 +836599at2759 +83779at2759 +844748at2759 +855834at2759 +858842at2759 +865202at2759 +866359at2759 +869548at2759 +878143at2759 +87842at2759 +887370at2759 +891751at2759 +898782at2759 +901894at2759 +905026at2759 +911863at2759 +917326at2759 +918816at2759 +919955at2759 +923657at2759 +924753at2759 +931188at2759 +937275at2759 +937686at2759 +939345at2759 +944899at2759 +946128at2759 +956854at2759 +97116at2759 +973442at2759 +974865at2759 +975158at2759 +975557at2759 +976469at2759 +981902at2759 +996662at2759 |
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| diff -r 0d243f458b53 -r 1278204240d8 test-data/genome_results_metaeuk_auto/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk_auto/short_summary Tue Nov 02 09:40:29 2021 +0000 |
| [ |
| @@ -0,0 +1,20 @@ +# BUSCO version is: 5.2.2 +# 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/tmp5e3tdhzs/files/c/9/b/dataset_c9b61090-5a2d-4dd0-8fd1-d147a4e1573c.dat +# BUSCO was run in mode: genome +# Gene predictor used: metaeuk + + ***** Results: ***** + + C:0.4%[S:0.4%,D:0.0%],F:0.0%,M:99.6%,n:255 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 254 Missing BUSCOs (M) + 255 Total BUSCO groups searched + +Dependencies and versions: + hmmsearch: 3.1 + prodigal: 2.6.3 + metaeuk: 5.34c21f2 |
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| diff -r 0d243f458b53 -r 1278204240d8 test-data/genome_results_metaeuk_auto/summary.png |
| b |
| Binary file test-data/genome_results_metaeuk_auto/summary.png has changed |
