| Previous changeset 4:0ea86ba426e1 (2025-06-17) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit ea21e425f6a04a586626c4a6d848aed1d1261b30 |
|
modified:
macros.xml taxonomy_wf.xml |
|
removed:
test-data/life.loc tool-data/class.loc.sample tool-data/domain.loc.sample tool-data/family.loc.sample tool-data/genus.loc.sample tool-data/life.loc.sample tool-data/order.loc.sample tool-data/phylum.loc.sample tool-data/species.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 macros.xml --- a/macros.xml Tue Jun 17 12:57:06 2025 +0000 +++ b/macros.xml Sat Aug 16 10:23:50 2025 +0000 |
| b |
| b'@@ -1,8 +1,8 @@\n <?xml version="1.0"?>\n <macros>\n <token name="@TOOL_VERSION@">1.2.4</token>\n- <token name="@VERSION_SUFFIX@">1</token>\n- <token name="@PROFILE@">21.01</token>\n+ <token name="@VERSION_SUFFIX@">2</token>\n+ <token name="@PROFILE@">24.0</token>\n <xml name="biotools">\n <xrefs>\n <xref type="bio.tools">checkm</xref>\n@@ -135,51 +135,1402 @@\n </param>\n <when value="life">\n <param name="taxon" type="select" label="Taxon of interest" >\n- <options from_data_table="life_taxons">\n- <validator message="No taxon database is available" type="no_options" />\n- </options>\n+ <option value="Prokaryote">Prokaryote (5656 genomes, 56 marker genes, 24 marker sets)</option>\n </param>\n </when>\n <when value="domain">\n <param name="taxon" type="select" label="Taxon of interest" >\n- <options from_data_table="domain_taxons">\n- <validator message="No taxon database is available" type="no_options" />\n- </options>\n+ <option value="Archaea">Archaea (207 genomes, 149 marker genes, 107 marker sets)</option>\n+ <option value="Bacteria">Bacteria (5449 genomes, 104 marker genes, 58 marker sets)</option>\n </param>\n </when>\n <when value="phylum">\n <param name="taxon" type="select" label="Taxon of interest" >\n- <options from_data_table="phylum_taxons">\n- <validator message="No taxon database is available" type="no_options" />\n- </options>\n+ <option value="Acidobacteria">Acidobacteria (15 genomes, 399 marker genes, 276 marker sets)</option>\n+ <option value="Actinobacteria">Actinobacteria (731 genomes, 204 marker genes, 119 marker sets)</option>\n+ <option value="Aquificae">Aquificae (18 genomes, 486 marker genes, 369 marker sets)</option>\n+ <option value="Bacteroidetes">Bacteroidetes (419 genomes, 286 marker genes, 195 marker sets)</option>\n+ <option value="Chlamydiae">Chlamydiae (64 genomes, 455 marker genes, 185 marker sets)</option>\n+ <option value="Chlorobi">Chlorobi (12 genomes, 612 marker genes, 333 marker sets)</option>\n+ <option value="Chloroflexi">Chloroflexi (20 genomes, 225 marker genes, 149 marker sets)</option>\n+ <option value="Crenarchaeota">Crenarchaeota (54 genomes, 217 marker genes, 168 marker sets)</option>\n+ <option value="Cyanobacteria">Cyanobacteria (129 genomes, 472 marker genes, 368 marker sets)</option>\n+ <option value="Deferribacteres">Deferribacteres (6 genomes, 564 marker genes, 339 marker sets)</option>\n+ <option value="Deinococcus-Thermus">Deinococcus-Thermus (40 genomes, 528 marker genes, 359 marker sets)</option>\n+ <option value="Dictyoglomi">Dictyoglomi (2 genomes, 1060 marker genes, 103 marker sets)</option>\n+ <option value="Euryarchaeota">Euryarchaeota (146 genomes, 188 marker genes, 125 marker sets)</option>\n+ <option value="Firmicutes">Firmicutes (1349 genomes, 172 marker genes, 99 marker sets)</option>\n+ <option value="Fusobacteria">Fusobacteria (32 genomes, 289 marker genes, 159 marker sets)</option>\n+ <option value="Ignavibacteriae">Ignavibacteriae (2 genomes, 1003 marker genes, 383 marker sets)</option>\n+ <option value="Nitrospirae">Nitrospirae (4 genomes, 676 marker genes, 379 marker sets)</option>\n+ <option value="Planctomycetes">Planctomycetes (11 genomes, 360 marker genes, 256 marker sets)</option>\n+ <option value="Proteobacteria">Pro'..b'alkalivibrio thiocyanoxidans (2 genomes, 1159 marker genes, 330 marker sets)</option>\n+ <option value="Thiobacillus denitrificans">Thiobacillus denitrificans (2 genomes, 1290 marker genes, 203 marker sets)</option>\n+ <option value="Treponema denticola">Treponema denticola (9 genomes, 954 marker genes, 221 marker sets)</option>\n+ <option value="Treponema pallidum">Treponema pallidum (3 genomes, 717 marker genes, 44 marker sets)</option>\n+ <option value="Treponema vincentii">Treponema vincentii (2 genomes, 946 marker genes, 178 marker sets)</option>\n+ <option value="Ureaplasma parvum">Ureaplasma parvum (5 genomes, 420 marker genes, 35 marker sets)</option>\n+ <option value="Ureaplasma urealyticum">Ureaplasma urealyticum (10 genomes, 386 marker genes, 50 marker sets)</option>\n+ <option value="Variovorax paradoxus">Variovorax paradoxus (5 genomes, 1314 marker genes, 368 marker sets)</option>\n+ <option value="Veillonella atypica">Veillonella atypica (3 genomes, 1145 marker genes, 136 marker sets)</option>\n+ <option value="Veillonella parvula">Veillonella parvula (2 genomes, 1174 marker genes, 97 marker sets)</option>\n+ <option value="Vibrio alginolyticus">Vibrio alginolyticus (5 genomes, 1283 marker genes, 392 marker sets)</option>\n+ <option value="Vibrio cholerae">Vibrio cholerae (20 genomes, 1729 marker genes, 348 marker sets)</option>\n+ <option value="Vibrio fischeri">Vibrio fischeri (2 genomes, 1814 marker genes, 227 marker sets)</option>\n+ <option value="Vibrio harveyi">Vibrio harveyi (3 genomes, 1674 marker genes, 373 marker sets)</option>\n+ <option value="Vibrio mimicus">Vibrio mimicus (2 genomes, 1752 marker genes, 276 marker sets)</option>\n+ <option value="Vibrio parahaemolyticus">Vibrio parahaemolyticus (12 genomes, 1733 marker genes, 363 marker sets)</option>\n+ <option value="Vibrio splendidus">Vibrio splendidus (2 genomes, 1757 marker genes, 310 marker sets)</option>\n+ <option value="Vibrio vulnificus">Vibrio vulnificus (5 genomes, 1802 marker genes, 386 marker sets)</option>\n+ <option value="Wigglesworthia glossinidia">Wigglesworthia glossinidia (2 genomes, 679 marker genes, 9 marker sets)</option>\n+ <option value="Wohlfahrtiimonas chitiniclastica">Wohlfahrtiimonas chitiniclastica (2 genomes, 1335 marker genes, 78 marker sets)</option>\n+ <option value="Wolbachia endosymbiont of Culex quinquefasciatus">Wolbachia endosymbiont of Culex quinquefasciatus (2 genomes, 747 marker genes, 56 marker sets)</option>\n+ <option value="Xanthomonas axonopodis">Xanthomonas axonopodis (5 genomes, 1627 marker genes, 365 marker sets)</option>\n+ <option value="Xanthomonas campestris">Xanthomonas campestris (5 genomes, 1623 marker genes, 336 marker sets)</option>\n+ <option value="Xanthomonas oryzae">Xanthomonas oryzae (3 genomes, 1627 marker genes, 339 marker sets)</option>\n+ <option value="Xylella fastidiosa">Xylella fastidiosa (10 genomes, 1207 marker genes, 178 marker sets)</option>\n+ <option value="Yersinia enterocolitica">Yersinia enterocolitica (5 genomes, 1868 marker genes, 316 marker sets)</option>\n+ <option value="Yersinia pestis">Yersinia pestis (20 genomes, 1683 marker genes, 330 marker sets)</option>\n+ <option value="Yersinia pseudotuberculosis">Yersinia pseudotuberculosis (4 genomes, 1975 marker genes, 263 marker sets)</option>\n+ <option value="Zymomonas mobilis">Zymomonas mobilis (3 genomes, 1142 marker genes, 133 marker sets)</option>\n </param>\n </when>\n </conditional>\n' |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 taxonomy_wf.xml --- a/taxonomy_wf.xml Tue Jun 17 12:57:06 2025 +0000 +++ b/taxonomy_wf.xml Sat Aug 16 10:23:50 2025 +0000 |
| b |
| @@ -13,7 +13,7 @@ checkm taxonomy_wf '$rank_taxon.rank' - '$rank_taxon.taxon.fields.value' + '$rank_taxon.taxon' 'bins' 'output' $analyze.ali |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 test-data/life.loc --- a/test-data/life.loc Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -# File generated by format_taxon_list.py script -# taxon description -Prokaryote Prokaryote (5656 genomes, 56 marker genes, 24 marker sets) |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/class.loc.sample --- a/tool-data/class.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,57 +0,0 @@ -# File generated by format_taxon_list.py script -# taxon description -Acidobacteriia Acidobacteriia (10 genomes, 572 marker genes, 395 marker sets) -Aciduliprofundum Aciduliprofundum (2 genomes, 763 marker genes, 130 marker sets) -Actinobacteria Actinobacteria (729 genomes, 205 marker genes, 119 marker sets) -Alphaproteobacteria Alphaproteobacteria (648 genomes, 225 marker genes, 148 marker sets) -Aquificae Aquificae (18 genomes, 486 marker genes, 369 marker sets) -Archaeoglobi Archaeoglobi (5 genomes, 619 marker genes, 392 marker sets) -Bacilli Bacilli (821 genomes, 250 marker genes, 136 marker sets) -Bacteroidetes Order II. Incertae sedis Bacteroidetes Order II. Incertae sedis (5 genomes, 801 marker genes, 466 marker sets) -Bacteroidia Bacteroidia (211 genomes, 401 marker genes, 266 marker sets) -Betaproteobacteria Betaproteobacteria (322 genomes, 387 marker genes, 234 marker sets) -Chlamydiia Chlamydiia (64 genomes, 455 marker genes, 185 marker sets) -Chlorobia Chlorobia (12 genomes, 612 marker genes, 333 marker sets) -Chloroflexi Chloroflexi (9 genomes, 452 marker genes, 315 marker sets) -Chroococcales Chroococcales (55 genomes, 490 marker genes, 378 marker sets) -Clostridia Clostridia (446 genomes, 196 marker genes, 110 marker sets) -Cytophagia Cytophagia (48 genomes, 438 marker genes, 328 marker sets) -Deferribacteres Deferribacteres (6 genomes, 564 marker genes, 339 marker sets) -Dehalococcoidetes Dehalococcoidetes (5 genomes, 755 marker genes, 54 marker sets) -Deinococci Deinococci (40 genomes, 528 marker genes, 359 marker sets) -Deltaproteobacteria Deltaproteobacteria (93 genomes, 197 marker genes, 125 marker sets) -Dictyoglomia Dictyoglomia (2 genomes, 1060 marker genes, 103 marker sets) -Epsilonproteobacteria Epsilonproteobacteria (111 genomes, 445 marker genes, 271 marker sets) -Erysipelotrichi Erysipelotrichi (18 genomes, 301 marker genes, 159 marker sets) -Flavobacteriia Flavobacteriia (126 genomes, 321 marker genes, 202 marker sets) -Fusobacteriia Fusobacteriia (32 genomes, 289 marker genes, 159 marker sets) -Gammaproteobacteria Gammaproteobacteria (1167 genomes, 280 marker genes, 178 marker sets) -Halobacteria Halobacteria (59 genomes, 367 marker genes, 241 marker sets) -Holophagae Holophagae (2 genomes, 883 marker genes, 459 marker sets) -Ignavibacteria Ignavibacteria (2 genomes, 1003 marker genes, 383 marker sets) -Methanobacteria Methanobacteria (12 genomes, 513 marker genes, 264 marker sets) -Methanococci Methanococci (16 genomes, 610 marker genes, 439 marker sets) -Methanomicrobia Methanomicrobia (29 genomes, 248 marker genes, 165 marker sets) -Mollicutes Mollicutes (119 genomes, 177 marker genes, 105 marker sets) -Negativicutes Negativicutes (64 genomes, 334 marker genes, 167 marker sets) -Nitrosopumilales Nitrosopumilales (2 genomes, 714 marker genes, 109 marker sets) -Nitrospira Nitrospira (4 genomes, 676 marker genes, 379 marker sets) -Nostocales Nostocales (18 genomes, 732 marker genes, 508 marker sets) -Opitutae Opitutae (4 genomes, 676 marker genes, 427 marker sets) -Oscillatoriales Oscillatoriales (25 genomes, 545 marker genes, 415 marker sets) -Planctomycetia Planctomycetia (11 genomes, 360 marker genes, 256 marker sets) -Pleurocapsales Pleurocapsales (6 genomes, 840 marker genes, 624 marker sets) -Prochlorales Prochlorales (18 genomes, 806 marker genes, 240 marker sets) -Solirubrobacterales Solirubrobacterales (2 genomes, 995 marker genes, 398 marker sets) -Sphingobacteriia Sphingobacteriia (27 genomes, 334 marker genes, 233 marker sets) -Spirochaetia Spirochaetia (71 genomes, 218 marker genes, 127 marker sets) -Stigonematales Stigonematales (5 genomes, 1007 marker genes, 576 marker sets) -Synergistia Synergistia (13 genomes, 452 marker genes, 160 marker sets) -Thermococci Thermococci (16 genomes, 500 marker genes, 315 marker sets) -Thermodesulfobacteria Thermodesulfobacteria (5 genomes, 813 marker genes, 440 marker sets) -Thermomicrobia Thermomicrobia (2 genomes, 933 marker genes, 336 marker sets) -Thermoplasmata Thermoplasmata (4 genomes, 563 marker genes, 310 marker sets) -Thermoprotei Thermoprotei (54 genomes, 217 marker genes, 168 marker sets) -Thermotogae Thermotogae (14 genomes, 460 marker genes, 267 marker sets) -Verrucomicrobiae Verrucomicrobiae (7 genomes, 403 marker genes, 284 marker sets) -Zetaproteobacteria Zetaproteobacteria (2 genomes, 1329 marker genes, 184 marker sets) |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/domain.loc.sample --- a/tool-data/domain.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -# File generated by format_taxon_list.py script -# taxon description -Archaea Archaea (207 genomes, 149 marker genes, 107 marker sets) -Bacteria Bacteria (5449 genomes, 104 marker genes, 58 marker sets) |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/family.loc.sample --- a/tool-data/family.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,233 +0,0 @@\n-# File generated by format_taxon_list.py script\n-# taxon\tdescription\n-Acetobacteraceae\tAcetobacteraceae (30 genomes, 473 marker genes, 264 marker sets)\n-Acholeplasmataceae\tAcholeplasmataceae (12 genomes, 176 marker genes, 88 marker sets)\n-Acidaminococcaceae\tAcidaminococcaceae (7 genomes, 677 marker genes, 256 marker sets)\n-Acidilobaceae\tAcidilobaceae (2 genomes, 645 marker genes, 144 marker sets)\n-Acidithiobacillaceae\tAcidithiobacillaceae (5 genomes, 907 marker genes, 200 marker sets)\n-Acidobacteriaceae\tAcidobacteriaceae (9 genomes, 575 marker genes, 396 marker sets)\n-Aciduliprofundum\tAciduliprofundum (2 genomes, 763 marker genes, 130 marker sets)\n-Actinomycetaceae\tActinomycetaceae (42 genomes, 420 marker genes, 211 marker sets)\n-Actinopolysporaceae\tActinopolysporaceae (3 genomes, 872 marker genes, 433 marker sets)\n-Aerococcaceae\tAerococcaceae (10 genomes, 424 marker genes, 195 marker sets)\n-Aeromonadaceae\tAeromonadaceae (17 genomes, 841 marker genes, 368 marker sets)\n-Alcaligenaceae\tAlcaligenaceae (27 genomes, 486 marker genes, 218 marker sets)\n-Alcanivoracaceae\tAlcanivoracaceae (8 genomes, 877 marker genes, 350 marker sets)\n-Alicyclobacillaceae\tAlicyclobacillaceae (9 genomes, 608 marker genes, 229 marker sets)\n-Alteromonadaceae\tAlteromonadaceae (38 genomes, 590 marker genes, 296 marker sets)\n-Anaplasmataceae\tAnaplasmataceae (18 genomes, 319 marker genes, 212 marker sets)\n-Aquificaceae\tAquificaceae (10 genomes, 656 marker genes, 475 marker sets)\n-Archaeoglobaceae\tArchaeoglobaceae (5 genomes, 619 marker genes, 392 marker sets)\n-Arthrospira\tArthrospira (2 genomes, 1432 marker genes, 419 marker sets)\n-Aurantimonadaceae\tAurantimonadaceae (4 genomes, 883 marker genes, 434 marker sets)\n-Bacillaceae\tBacillaceae (162 genomes, 418 marker genes, 155 marker sets)\n-Bacteroidaceae\tBacteroidaceae (96 genomes, 524 marker genes, 282 marker sets)\n-Bankia\tBankia (2 genomes, 1388 marker genes, 332 marker sets)\n-Bartonellaceae\tBartonellaceae (29 genomes, 708 marker genes, 188 marker sets)\n-Bdellovibrionaceae\tBdellovibrionaceae (4 genomes, 561 marker genes, 331 marker sets)\n-Beijerinckiaceae\tBeijerinckiaceae (4 genomes, 1024 marker genes, 488 marker sets)\n-Bifidobacteriaceae\tBifidobacteriaceae (77 genomes, 464 marker genes, 220 marker sets)\n-Blattabacteriaceae\tBlattabacteriaceae (6 genomes, 547 marker genes, 16 marker sets)\n-Brachyspiraceae\tBrachyspiraceae (10 genomes, 783 marker genes, 458 marker sets)\n-Bradyrhizobiaceae\tBradyrhizobiaceae (52 genomes, 619 marker genes, 276 marker sets)\n-Brevibacteriaceae\tBrevibacteriaceae (3 genomes, 833 marker genes, 259 marker sets)\n-Brucellaceae\tBrucellaceae (94 genomes, 1206 marker genes, 241 marker sets)\n-Burkholderiaceae\tBurkholderiaceae (94 genomes, 568 marker genes, 224 marker sets)\n-Campylobacteraceae\tCampylobacteraceae (66 genomes, 505 marker genes, 274 marker sets)\n-Cardiobacteriaceae\tCardiobacteriaceae (3 genomes, 807 marker genes, 349 marker sets)\n-Carnobacteriaceae\tCarnobacteriaceae (7 genomes, 469 marker genes, 197 marker sets)\n-Caulobacteraceae\tCaulobacteraceae (15 genomes, 644 marker genes, 366 marker sets)\n-Cellulomonadaceae\tCellulomonadaceae (7 genomes, 766 marker genes, 260 marker sets)\n-Chitinophagaceae\tChitinophagaceae (8 genomes, 634 marker genes, 396 marker sets)\n-Chlamydiaceae\tChlamydiaceae (59 genomes, 590 marker genes, 92 marker sets)\n-Chlorobiaceae\tChlorobiaceae (12 genomes, 612 marker genes, 333 marker sets)\n-Chloroflexaceae\tChloroflexaceae (7 genomes, 570 marker genes, 386 marker sets)\n-Chromatiaceae\tChromatiaceae (14 genomes, 545 marker genes, 300 marker sets)\n-Chroococcidiopsis\tChroococcidiopsis (2 genomes, 1159 marker genes, 811 marker sets)\n-Clostridiaceae\tClostridiaceae (10 genomes, 387 marker genes, 178 marker sets)\n-Clostridiales Family XI. Incertae Sedis\tClostridiales Family XI. Incertae Sedis (20 genomes, 345 marker genes, 186 marker sets)\n-Clostridiales Family XVII. Incertae Sedis\tClostridiales Family XVII. Incertae Sedis (5 genomes, 682 marker genes, 2'..b'2 genomes, 1121 marker genes, 424 marker sets)\n-Rhodocyclaceae\tRhodocyclaceae (25 genomes, 641 marker genes, 269 marker sets)\n-Rhodospirillaceae\tRhodospirillaceae (26 genomes, 300 marker genes, 163 marker sets)\n-Rhodothermaceae\tRhodothermaceae (5 genomes, 801 marker genes, 466 marker sets)\n-Rickettsiaceae\tRickettsiaceae (46 genomes, 528 marker genes, 196 marker sets)\n-Rikenellaceae\tRikenellaceae (6 genomes, 648 marker genes, 386 marker sets)\n-Rivulariaceae\tRivulariaceae (3 genomes, 1070 marker genes, 642 marker sets)\n-Rubrivivax\tRubrivivax (3 genomes, 1586 marker genes, 343 marker sets)\n-Rubrobacteraceae\tRubrobacteraceae (2 genomes, 991 marker genes, 269 marker sets)\n-Ruminococcaceae\tRuminococcaceae (20 genomes, 284 marker genes, 161 marker sets)\n-Saprospiraceae\tSaprospiraceae (5 genomes, 671 marker genes, 479 marker sets)\n-Shewanellaceae\tShewanellaceae (26 genomes, 989 marker genes, 339 marker sets)\n-Sinobacteraceae\tSinobacteraceae (4 genomes, 1083 marker genes, 398 marker sets)\n-Solirubrobacteraceae\tSolirubrobacteraceae (2 genomes, 995 marker genes, 398 marker sets)\n-Sphingobacteriaceae\tSphingobacteriaceae (11 genomes, 575 marker genes, 344 marker sets)\n-Sphingomonadaceae\tSphingomonadaceae (27 genomes, 501 marker genes, 275 marker sets)\n-Spirochaetaceae\tSpirochaetaceae (56 genomes, 235 marker genes, 124 marker sets)\n-Sporolactobacillaceae\tSporolactobacillaceae (2 genomes, 1066 marker genes, 320 marker sets)\n-Staphylococcaceae\tStaphylococcaceae (64 genomes, 642 marker genes, 181 marker sets)\n-Streptococcaceae\tStreptococcaceae (240 genomes, 524 marker genes, 282 marker sets)\n-Streptomycetaceae\tStreptomycetaceae (58 genomes, 506 marker genes, 264 marker sets)\n-Streptosporangiaceae\tStreptosporangiaceae (2 genomes, 1116 marker genes, 473 marker sets)\n-Succinivibrionaceae\tSuccinivibrionaceae (6 genomes, 637 marker genes, 317 marker sets)\n-Sulfolobaceae\tSulfolobaceae (19 genomes, 526 marker genes, 149 marker sets)\n-Sutterellaceae\tSutterellaceae (4 genomes, 792 marker genes, 261 marker sets)\n-Synechococcus\tSynechococcus (25 genomes, 554 marker genes, 425 marker sets)\n-Synechocystis\tSynechocystis (5 genomes, 1099 marker genes, 794 marker sets)\n-Synergistaceae\tSynergistaceae (13 genomes, 452 marker genes, 160 marker sets)\n-Syntrophomonadaceae\tSyntrophomonadaceae (3 genomes, 744 marker genes, 271 marker sets)\n-Teredinibacter\tTeredinibacter (10 genomes, 1162 marker genes, 360 marker sets)\n-Thermaceae\tThermaceae (23 genomes, 585 marker genes, 331 marker sets)\n-Thermoactinomycetaceae\tThermoactinomycetaceae (2 genomes, 1027 marker genes, 387 marker sets)\n-Thermoanaerobacteraceae\tThermoanaerobacteraceae (24 genomes, 438 marker genes, 193 marker sets)\n-Thermoanaerobacterales Family III. Incertae Sedis\tThermoanaerobacterales Family III. Incertae Sedis (16 genomes, 599 marker genes, 251 marker sets)\n-Thermococcaceae\tThermococcaceae (16 genomes, 500 marker genes, 315 marker sets)\n-Thermodesulfobacteriaceae\tThermodesulfobacteriaceae (5 genomes, 813 marker genes, 440 marker sets)\n-Thermodesulfobiaceae\tThermodesulfobiaceae (3 genomes, 538 marker genes, 284 marker sets)\n-Thermomonosporaceae\tThermomonosporaceae (4 genomes, 839 marker genes, 346 marker sets)\n-Thermoplasmataceae\tThermoplasmataceae (2 genomes, 733 marker genes, 167 marker sets)\n-Thermoproteaceae\tThermoproteaceae (12 genomes, 410 marker genes, 333 marker sets)\n-Thermotogaceae\tThermotogaceae (14 genomes, 460 marker genes, 267 marker sets)\n-Thiomonas\tThiomonas (3 genomes, 1202 marker genes, 366 marker sets)\n-Thiotrichaceae\tThiotrichaceae (6 genomes, 764 marker genes, 473 marker sets)\n-Veillonellaceae\tVeillonellaceae (57 genomes, 345 marker genes, 171 marker sets)\n-Verrucomicrobiaceae\tVerrucomicrobiaceae (5 genomes, 505 marker genes, 342 marker sets)\n-Vibrionaceae\tVibrionaceae (80 genomes, 922 marker genes, 367 marker sets)\n-Xanthobacteraceae\tXanthobacteraceae (9 genomes, 824 marker genes, 433 marker sets)\n-Xanthomonadaceae\tXanthomonadaceae (58 genomes, 540 marker genes, 311 marker sets)\n' |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/genus.loc.sample --- a/tool-data/genus.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,508 +0,0 @@\n-# File generated by format_taxon_list.py script\n-# taxon\tdescription\n-Acetobacter\tAcetobacter (11 genomes, 1037 marker genes, 392 marker sets)\n-Acholeplasma\tAcholeplasma (7 genomes, 309 marker genes, 151 marker sets)\n-Achromobacter\tAchromobacter (5 genomes, 1298 marker genes, 427 marker sets)\n-Acidaminococcus\tAcidaminococcus (5 genomes, 910 marker genes, 256 marker sets)\n-Acidilobus\tAcidilobus (2 genomes, 645 marker genes, 144 marker sets)\n-Acidiphilium\tAcidiphilium (3 genomes, 1244 marker genes, 339 marker sets)\n-Acidithiobacillus\tAcidithiobacillus (5 genomes, 907 marker genes, 200 marker sets)\n-Acidobacterium\tAcidobacterium (2 genomes, 1151 marker genes, 582 marker sets)\n-Acidovorax\tAcidovorax (9 genomes, 931 marker genes, 335 marker sets)\n-Aciduliprofundum\tAciduliprofundum (2 genomes, 763 marker genes, 130 marker sets)\n-Acinetobacter\tAcinetobacter (66 genomes, 883 marker genes, 281 marker sets)\n-Actinobacillus\tActinobacillus (18 genomes, 1004 marker genes, 589 marker sets)\n-Actinobaculum\tActinobaculum (5 genomes, 606 marker genes, 222 marker sets)\n-Actinomadura\tActinomadura (3 genomes, 940 marker genes, 376 marker sets)\n-Actinomyces\tActinomyces (27 genomes, 432 marker genes, 214 marker sets)\n-Actinoplanes\tActinoplanes (3 genomes, 1041 marker genes, 394 marker sets)\n-Actinopolyspora\tActinopolyspora (3 genomes, 872 marker genes, 433 marker sets)\n-Aequorivita\tAequorivita (2 genomes, 1087 marker genes, 283 marker sets)\n-Aerococcus\tAerococcus (2 genomes, 719 marker genes, 247 marker sets)\n-Aeromonas\tAeromonas (12 genomes, 1380 marker genes, 463 marker sets)\n-Aggregatibacter\tAggregatibacter (13 genomes, 991 marker genes, 357 marker sets)\n-Agrobacterium\tAgrobacterium (12 genomes, 994 marker genes, 379 marker sets)\n-Agromyces\tAgromyces (2 genomes, 1096 marker genes, 287 marker sets)\n-Ahrensia\tAhrensia (2 genomes, 1213 marker genes, 422 marker sets)\n-Alcaligenes\tAlcaligenes (2 genomes, 1577 marker genes, 235 marker sets)\n-Alcanivorax\tAlcanivorax (6 genomes, 1175 marker genes, 317 marker sets)\n-Algoriphagus\tAlgoriphagus (5 genomes, 947 marker genes, 361 marker sets)\n-Aliagarivorans\tAliagarivorans (2 genomes, 1740 marker genes, 251 marker sets)\n-Alicycliphilus\tAlicycliphilus (2 genomes, 1650 marker genes, 258 marker sets)\n-Alicyclobacillus\tAlicyclobacillus (8 genomes, 664 marker genes, 240 marker sets)\n-Alishewanella\tAlishewanella (2 genomes, 1677 marker genes, 232 marker sets)\n-Alistipes\tAlistipes (5 genomes, 703 marker genes, 335 marker sets)\n-Alkaliphilus\tAlkaliphilus (2 genomes, 970 marker genes, 326 marker sets)\n-Alloscardovia\tAlloscardovia (2 genomes, 950 marker genes, 116 marker sets)\n-Alteromonas\tAlteromonas (6 genomes, 1419 marker genes, 314 marker sets)\n-Aminobacterium\tAminobacterium (2 genomes, 950 marker genes, 145 marker sets)\n-Amycolatopsis\tAmycolatopsis (12 genomes, 644 marker genes, 302 marker sets)\n-Anabaena\tAnabaena (5 genomes, 992 marker genes, 584 marker sets)\n-Anaerococcus\tAnaerococcus (6 genomes, 665 marker genes, 181 marker sets)\n-Anaeromyxobacter\tAnaeromyxobacter (4 genomes, 1162 marker genes, 375 marker sets)\n-Anaplasma\tAnaplasma (2 genomes, 688 marker genes, 127 marker sets)\n-Anoxybacillus\tAnoxybacillus (5 genomes, 1141 marker genes, 212 marker sets)\n-Aquimarina\tAquimarina (2 genomes, 1084 marker genes, 373 marker sets)\n-Archaeoglobus\tArchaeoglobus (4 genomes, 662 marker genes, 415 marker sets)\n-Arcobacter\tArcobacter (8 genomes, 804 marker genes, 234 marker sets)\n-Arenibacter\tArenibacter (2 genomes, 1200 marker genes, 269 marker sets)\n-Arsenophonus\tArsenophonus (4 genomes, 640 marker genes, 164 marker sets)\n-Arthrobacter\tArthrobacter (25 genomes, 473 marker genes, 190 marker sets)\n-Arthrospira\tArthrospira (2 genomes, 1432 marker genes, 419 marker sets)\n-Asticcacaulis\tAsticcacaulis (3 genomes, 1116 marker genes, 409 marker sets)\n-Atopobium\tAtopobium (8 genomes, 486 marker genes, 194 marker sets)\n-Aurantimonas\tAurantimonas (2 genomes, 1288 marker genes, 356 marker sets)\n-Azoarcus\tAzoarcus (2'..b'erella\tSutterella (3 genomes, 935 marker genes, 232 marker sets)\n-Synechococcus\tSynechococcus (25 genomes, 554 marker genes, 425 marker sets)\n-Synechocystis\tSynechocystis (5 genomes, 1099 marker genes, 794 marker sets)\n-Tannerella\tTannerella (2 genomes, 822 marker genes, 441 marker sets)\n-Taylorella\tTaylorella (4 genomes, 1069 marker genes, 71 marker sets)\n-Tenacibaculum\tTenacibaculum (2 genomes, 1057 marker genes, 272 marker sets)\n-Teredinibacter\tTeredinibacter (10 genomes, 1162 marker genes, 360 marker sets)\n-Tetragenococcus\tTetragenococcus (2 genomes, 953 marker genes, 183 marker sets)\n-Thalassospira\tThalassospira (3 genomes, 1406 marker genes, 326 marker sets)\n-Thauera\tThauera (6 genomes, 1175 marker genes, 334 marker sets)\n-Thermacetogenium\tThermacetogenium (2 genomes, 1344 marker genes, 157 marker sets)\n-Thermaerobacter\tThermaerobacter (2 genomes, 1204 marker genes, 181 marker sets)\n-Thermanaerovibrio\tThermanaerovibrio (2 genomes, 1136 marker genes, 117 marker sets)\n-Thermoanaerobacter\tThermoanaerobacter (13 genomes, 976 marker genes, 195 marker sets)\n-Thermoanaerobacterium\tThermoanaerobacterium (4 genomes, 1117 marker genes, 147 marker sets)\n-Thermobifida\tThermobifida (2 genomes, 1421 marker genes, 225 marker sets)\n-Thermococcus\tThermococcus (9 genomes, 552 marker genes, 286 marker sets)\n-Thermocrinis\tThermocrinis (2 genomes, 941 marker genes, 515 marker sets)\n-Thermocrispum\tThermocrispum (2 genomes, 1264 marker genes, 288 marker sets)\n-Thermodesulfatator\tThermodesulfatator (2 genomes, 1149 marker genes, 333 marker sets)\n-Thermodesulfobacterium\tThermodesulfobacterium (3 genomes, 960 marker genes, 243 marker sets)\n-Thermodesulfovibrio\tThermodesulfovibrio (3 genomes, 999 marker genes, 215 marker sets)\n-Thermogladius\tThermogladius (2 genomes, 711 marker genes, 60 marker sets)\n-Thermoplasma\tThermoplasma (2 genomes, 733 marker genes, 167 marker sets)\n-Thermoproteus\tThermoproteus (3 genomes, 600 marker genes, 281 marker sets)\n-Thermosipho\tThermosipho (2 genomes, 1009 marker genes, 148 marker sets)\n-Thermotoga\tThermotoga (8 genomes, 768 marker genes, 325 marker sets)\n-Thermus\tThermus (14 genomes, 841 marker genes, 311 marker sets)\n-Thioalkalimicrobium\tThioalkalimicrobium (2 genomes, 1175 marker genes, 103 marker sets)\n-Thioalkalivibrio\tThioalkalivibrio (70 genomes, 1059 marker genes, 270 marker sets)\n-Thiobacillus\tThiobacillus (3 genomes, 1205 marker genes, 209 marker sets)\n-Thiomicrospira\tThiomicrospira (8 genomes, 954 marker genes, 243 marker sets)\n-Thiomonas\tThiomonas (3 genomes, 1202 marker genes, 366 marker sets)\n-Thiothrix\tThiothrix (4 genomes, 1003 marker genes, 417 marker sets)\n-Tolumonas\tTolumonas (2 genomes, 1431 marker genes, 200 marker sets)\n-Treponema\tTreponema (28 genomes, 326 marker genes, 173 marker sets)\n-Turicibacter\tTuricibacter (2 genomes, 1183 marker genes, 236 marker sets)\n-Ureaplasma\tUreaplasma (15 genomes, 372 marker genes, 51 marker sets)\n-Variovorax\tVariovorax (7 genomes, 1114 marker genes, 351 marker sets)\n-Veillonella\tVeillonella (13 genomes, 757 marker genes, 219 marker sets)\n-Verrucomicrobium\tVerrucomicrobium (3 genomes, 697 marker genes, 466 marker sets)\n-Vibrio\tVibrio (70 genomes, 1084 marker genes, 381 marker sets)\n-Vulcanisaeta\tVulcanisaeta (2 genomes, 713 marker genes, 173 marker sets)\n-Weissella\tWeissella (6 genomes, 534 marker genes, 171 marker sets)\n-Wigglesworthia\tWigglesworthia (2 genomes, 679 marker genes, 9 marker sets)\n-Wohlfahrtiimonas\tWohlfahrtiimonas (2 genomes, 1335 marker genes, 78 marker sets)\n-Wolbachia\tWolbachia (8 genomes, 427 marker genes, 275 marker sets)\n-Xanthobacter\tXanthobacter (3 genomes, 1394 marker genes, 374 marker sets)\n-Xanthomonas\tXanthomonas (16 genomes, 1163 marker genes, 401 marker sets)\n-Xenorhabdus\tXenorhabdus (2 genomes, 1608 marker genes, 267 marker sets)\n-Xylella\tXylella (10 genomes, 1207 marker genes, 178 marker sets)\n-Yersinia\tYersinia (35 genomes, 1383 marker genes, 341 marker sets)\n-Zymomonas\tZymomonas (3 genomes, 1142 marker genes, 133 marker sets)\n' |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/life.loc.sample --- a/tool-data/life.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -# File generated by format_taxon_list.py script -# taxon description -Prokaryote Prokaryote (5656 genomes, 56 marker genes, 24 marker sets) |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/order.loc.sample --- a/tool-data/order.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,100 +0,0 @@\n-# File generated by format_taxon_list.py script\n-# taxon\tdescription\n-Acholeplasmatales\tAcholeplasmatales (12 genomes, 176 marker genes, 88 marker sets)\n-Acidilobales\tAcidilobales (3 genomes, 558 marker genes, 236 marker sets)\n-Acidithiobacillales\tAcidithiobacillales (6 genomes, 795 marker genes, 254 marker sets)\n-Acidobacteriales\tAcidobacteriales (10 genomes, 572 marker genes, 395 marker sets)\n-Aciduliprofundum\tAciduliprofundum (2 genomes, 763 marker genes, 130 marker sets)\n-Actinomycetales\tActinomycetales (620 genomes, 256 marker genes, 152 marker sets)\n-Aeromonadales\tAeromonadales (23 genomes, 456 marker genes, 237 marker sets)\n-Alteromonadales\tAlteromonadales (116 genomes, 519 marker genes, 267 marker sets)\n-Aquificales\tAquificales (18 genomes, 486 marker genes, 369 marker sets)\n-Archaeoglobales\tArchaeoglobales (5 genomes, 619 marker genes, 392 marker sets)\n-Bacillales\tBacillales (331 genomes, 319 marker genes, 134 marker sets)\n-Bacteroidales\tBacteroidales (210 genomes, 402 marker genes, 267 marker sets)\n-Bacteroidetes Order II. Incertae sedis\tBacteroidetes Order II. Incertae sedis (5 genomes, 801 marker genes, 466 marker sets)\n-Bankia\tBankia (2 genomes, 1388 marker genes, 332 marker sets)\n-Bdellovibrionales\tBdellovibrionales (5 genomes, 466 marker genes, 290 marker sets)\n-Bifidobacteriales\tBifidobacteriales (77 genomes, 464 marker genes, 220 marker sets)\n-Burkholderiales\tBurkholderiales (194 genomes, 427 marker genes, 216 marker sets)\n-Campylobacterales\tCampylobacterales (107 genomes, 458 marker genes, 273 marker sets)\n-Cardiobacteriales\tCardiobacteriales (3 genomes, 807 marker genes, 349 marker sets)\n-Caulobacterales\tCaulobacterales (15 genomes, 644 marker genes, 366 marker sets)\n-Chlamydiales\tChlamydiales (64 genomes, 455 marker genes, 185 marker sets)\n-Chlorobiales\tChlorobiales (12 genomes, 612 marker genes, 333 marker sets)\n-Chloroflexales\tChloroflexales (8 genomes, 501 marker genes, 342 marker sets)\n-Chromatiales\tChromatiales (92 genomes, 595 marker genes, 283 marker sets)\n-Chroococcales\tChroococcales (55 genomes, 490 marker genes, 378 marker sets)\n-Clostridiales\tClostridiales (395 genomes, 202 marker genes, 114 marker sets)\n-Coriobacteriales\tCoriobacteriales (23 genomes, 304 marker genes, 155 marker sets)\n-Cytophagales\tCytophagales (48 genomes, 438 marker genes, 328 marker sets)\n-Deferribacterales\tDeferribacterales (6 genomes, 564 marker genes, 339 marker sets)\n-Dehalococcoidales\tDehalococcoidales (5 genomes, 755 marker genes, 54 marker sets)\n-Deinococcales\tDeinococcales (17 genomes, 563 marker genes, 388 marker sets)\n-Desulfobacterales\tDesulfobacterales (20 genomes, 320 marker genes, 189 marker sets)\n-Desulfovibrionales\tDesulfovibrionales (40 genomes, 454 marker genes, 252 marker sets)\n-Desulfurellales\tDesulfurellales (4 genomes, 817 marker genes, 252 marker sets)\n-Desulfurococcales\tDesulfurococcales (14 genomes, 287 marker genes, 213 marker sets)\n-Desulfuromonadales\tDesulfuromonadales (13 genomes, 550 marker genes, 283 marker sets)\n-Dictyoglomales\tDictyoglomales (2 genomes, 1060 marker genes, 103 marker sets)\n-Enterobacteriales\tEnterobacteriales (262 genomes, 297 marker genes, 121 marker sets)\n-Entomoplasmatales\tEntomoplasmatales (9 genomes, 362 marker genes, 151 marker sets)\n-Erysipelotrichales\tErysipelotrichales (18 genomes, 301 marker genes, 159 marker sets)\n-Flavobacteriales\tFlavobacteriales (126 genomes, 321 marker genes, 202 marker sets)\n-Fusobacteriales\tFusobacteriales (32 genomes, 289 marker genes, 159 marker sets)\n-Halanaerobiales\tHalanaerobiales (7 genomes, 504 marker genes, 189 marker sets)\n-Halobacteriales\tHalobacteriales (59 genomes, 367 marker genes, 241 marker sets)\n-Holophagales\tHolophagales (2 genomes, 883 marker genes, 459 marker sets)\n-Hydrogenophilales\tHydrogenophilales (3 genomes, 1205 marker genes, 209 marker sets)\n-Ignavibacteriales\tIgnavibacteriales (2 genomes, 1003 marker genes, 383 marker sets)\n-Lactobacillales\tLactobacillales (490 genomes, 335 marker genes, 183 marker'..b'lales\tLegionellales (23 genomes, 545 marker genes, 269 marker sets)\n-Mariprofundales\tMariprofundales (2 genomes, 1329 marker genes, 184 marker sets)\n-Methanobacteriales\tMethanobacteriales (12 genomes, 513 marker genes, 264 marker sets)\n-Methanocellales\tMethanocellales (3 genomes, 712 marker genes, 317 marker sets)\n-Methanococcales\tMethanococcales (16 genomes, 610 marker genes, 439 marker sets)\n-Methanomicrobiales\tMethanomicrobiales (11 genomes, 465 marker genes, 230 marker sets)\n-Methanosarcinales\tMethanosarcinales (14 genomes, 438 marker genes, 270 marker sets)\n-Methylococcales\tMethylococcales (15 genomes, 684 marker genes, 348 marker sets)\n-Methylophilales\tMethylophilales (16 genomes, 685 marker genes, 234 marker sets)\n-Mycoplasmatales\tMycoplasmatales (98 genomes, 217 marker genes, 127 marker sets)\n-Myxococcales\tMyxococcales (8 genomes, 534 marker genes, 348 marker sets)\n-Nautiliales\tNautiliales (4 genomes, 712 marker genes, 351 marker sets)\n-Neisseriales\tNeisseriales (69 genomes, 658 marker genes, 446 marker sets)\n-Nitrosomonadales\tNitrosomonadales (7 genomes, 851 marker genes, 314 marker sets)\n-Nitrosopumilales\tNitrosopumilales (2 genomes, 714 marker genes, 109 marker sets)\n-Nitrospirales\tNitrospirales (4 genomes, 676 marker genes, 379 marker sets)\n-Nostocales\tNostocales (18 genomes, 732 marker genes, 508 marker sets)\n-Oceanospirillales\tOceanospirillales (41 genomes, 497 marker genes, 229 marker sets)\n-Opitutales\tOpitutales (3 genomes, 859 marker genes, 521 marker sets)\n-Oscillatoriales\tOscillatoriales (25 genomes, 545 marker genes, 415 marker sets)\n-Pasteurellales\tPasteurellales (83 genomes, 767 marker genes, 440 marker sets)\n-Planctomycetales\tPlanctomycetales (10 genomes, 370 marker genes, 265 marker sets)\n-Pleurocapsales\tPleurocapsales (6 genomes, 840 marker genes, 624 marker sets)\n-Prochlorales\tProchlorales (18 genomes, 806 marker genes, 240 marker sets)\n-Pseudomonadales\tPseudomonadales (274 genomes, 549 marker genes, 326 marker sets)\n-Rhizobiales\tRhizobiales (349 genomes, 407 marker genes, 244 marker sets)\n-Rhodobacterales\tRhodobacterales (104 genomes, 504 marker genes, 327 marker sets)\n-Rhodocyclales\tRhodocyclales (26 genomes, 625 marker genes, 264 marker sets)\n-Rhodospirillales\tRhodospirillales (57 genomes, 367 marker genes, 228 marker sets)\n-Rickettsiales\tRickettsiales (81 genomes, 325 marker genes, 210 marker sets)\n-Rubrobacterales\tRubrobacterales (2 genomes, 991 marker genes, 269 marker sets)\n-Selenomonadales\tSelenomonadales (64 genomes, 334 marker genes, 167 marker sets)\n-Solirubrobacterales\tSolirubrobacterales (4 genomes, 721 marker genes, 307 marker sets)\n-Sphingobacteriales\tSphingobacteriales (27 genomes, 334 marker genes, 233 marker sets)\n-Sphingomonadales\tSphingomonadales (31 genomes, 490 marker genes, 270 marker sets)\n-Spirochaetales\tSpirochaetales (71 genomes, 218 marker genes, 127 marker sets)\n-Stigonematales\tStigonematales (5 genomes, 1007 marker genes, 576 marker sets)\n-Sulfolobales\tSulfolobales (20 genomes, 499 marker genes, 141 marker sets)\n-Synergistales\tSynergistales (13 genomes, 452 marker genes, 160 marker sets)\n-Thermales\tThermales (23 genomes, 585 marker genes, 331 marker sets)\n-Thermoanaerobacterales\tThermoanaerobacterales (44 genomes, 308 marker genes, 158 marker sets)\n-Thermococcales\tThermococcales (16 genomes, 500 marker genes, 315 marker sets)\n-Thermodesulfobacteriales\tThermodesulfobacteriales (5 genomes, 813 marker genes, 440 marker sets)\n-Thermoplasmatales\tThermoplasmatales (4 genomes, 563 marker genes, 310 marker sets)\n-Thermoproteales\tThermoproteales (13 genomes, 315 marker genes, 257 marker sets)\n-Thermotogales\tThermotogales (14 genomes, 460 marker genes, 267 marker sets)\n-Thiotrichales\tThiotrichales (64 genomes, 406 marker genes, 251 marker sets)\n-Verrucomicrobiales\tVerrucomicrobiales (7 genomes, 403 marker genes, 284 marker sets)\n-Vibrionales\tVibrionales (80 genomes, 922 marker genes, 367 marker sets)\n-Xanthomonadales\tXanthomonadales (63 genomes, 499 marker genes, 264 marker sets)\n' |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/phylum.loc.sample --- a/tool-data/phylum.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -# File generated by format_taxon_list.py script -# taxon description -Acidobacteria Acidobacteria (15 genomes, 399 marker genes, 276 marker sets) -Actinobacteria Actinobacteria (731 genomes, 204 marker genes, 119 marker sets) -Aquificae Aquificae (18 genomes, 486 marker genes, 369 marker sets) -Bacteroidetes Bacteroidetes (419 genomes, 286 marker genes, 195 marker sets) -Chlamydiae Chlamydiae (64 genomes, 455 marker genes, 185 marker sets) -Chlorobi Chlorobi (12 genomes, 612 marker genes, 333 marker sets) -Chloroflexi Chloroflexi (20 genomes, 225 marker genes, 149 marker sets) -Crenarchaeota Crenarchaeota (54 genomes, 217 marker genes, 168 marker sets) -Cyanobacteria Cyanobacteria (129 genomes, 472 marker genes, 368 marker sets) -Deferribacteres Deferribacteres (6 genomes, 564 marker genes, 339 marker sets) -Deinococcus-Thermus Deinococcus-Thermus (40 genomes, 528 marker genes, 359 marker sets) -Dictyoglomi Dictyoglomi (2 genomes, 1060 marker genes, 103 marker sets) -Euryarchaeota Euryarchaeota (146 genomes, 188 marker genes, 125 marker sets) -Firmicutes Firmicutes (1349 genomes, 172 marker genes, 99 marker sets) -Fusobacteria Fusobacteria (32 genomes, 289 marker genes, 159 marker sets) -Ignavibacteriae Ignavibacteriae (2 genomes, 1003 marker genes, 383 marker sets) -Nitrospirae Nitrospirae (4 genomes, 676 marker genes, 379 marker sets) -Planctomycetes Planctomycetes (11 genomes, 360 marker genes, 256 marker sets) -Proteobacteria Proteobacteria (2343 genomes, 182 marker genes, 119 marker sets) -Spirochaetes Spirochaetes (71 genomes, 218 marker genes, 127 marker sets) -Synergistetes Synergistetes (13 genomes, 452 marker genes, 160 marker sets) -Tenericutes Tenericutes (119 genomes, 177 marker genes, 105 marker sets) -Thaumarchaeota Thaumarchaeota (4 genomes, 548 marker genes, 265 marker sets) -Thermodesulfobacteria Thermodesulfobacteria (5 genomes, 813 marker genes, 440 marker sets) -Thermotogae Thermotogae (14 genomes, 460 marker genes, 267 marker sets) -Verrucomicrobia Verrucomicrobia (12 genomes, 346 marker genes, 245 marker sets) |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool-data/species.loc.sample --- a/tool-data/species.loc.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,510 +0,0 @@\n-# File generated by format_taxon_list.py script\n-# taxon\tdescription\n-Acetobacter pasteurianus\tAcetobacter pasteurianus (9 genomes, 1384 marker genes, 160 marker sets)\n-Achromobacter piechaudii\tAchromobacter piechaudii (2 genomes, 1606 marker genes, 428 marker sets)\n-Achromobacter xylosoxidans\tAchromobacter xylosoxidans (2 genomes, 1503 marker genes, 445 marker sets)\n-Acidaminococcus intestini\tAcidaminococcus intestini (2 genomes, 1109 marker genes, 140 marker sets)\n-Acidithiobacillus caldus\tAcidithiobacillus caldus (2 genomes, 1196 marker genes, 153 marker sets)\n-Acidithiobacillus ferrooxidans\tAcidithiobacillus ferrooxidans (2 genomes, 1293 marker genes, 128 marker sets)\n-Acidovorax avenae\tAcidovorax avenae (2 genomes, 1633 marker genes, 327 marker sets)\n-Acinetobacter baumanni\tAcinetobacter baumanni (5 genomes, 1413 marker genes, 231 marker sets)\n-Acinetobacter baumannii\tAcinetobacter baumannii (20 genomes, 1018 marker genes, 298 marker sets)\n-Acinetobacter baylyi\tAcinetobacter baylyi (2 genomes, 1608 marker genes, 195 marker sets)\n-Acinetobacter calcoaceticus\tAcinetobacter calcoaceticus (5 genomes, 1444 marker genes, 252 marker sets)\n-Acinetobacter johnsonii\tAcinetobacter johnsonii (2 genomes, 1439 marker genes, 204 marker sets)\n-Acinetobacter junii\tAcinetobacter junii (4 genomes, 1336 marker genes, 222 marker sets)\n-Acinetobacter lwoffii\tAcinetobacter lwoffii (3 genomes, 1363 marker genes, 221 marker sets)\n-Acinetobacter nosocomialis\tAcinetobacter nosocomialis (2 genomes, 1542 marker genes, 214 marker sets)\n-Acinetobacter radioresistens\tAcinetobacter radioresistens (5 genomes, 1354 marker genes, 199 marker sets)\n-Actinobacillus pleuropneumoniae\tActinobacillus pleuropneumoniae (13 genomes, 1332 marker genes, 210 marker sets)\n-Actinobaculum schaalii\tActinobaculum schaalii (2 genomes, 951 marker genes, 128 marker sets)\n-Actinomyces graevenitzii\tActinomyces graevenitzii (2 genomes, 1014 marker genes, 144 marker sets)\n-Actinomyces naeslundii\tActinomyces naeslundii (2 genomes, 1068 marker genes, 299 marker sets)\n-Actinomyces neuii\tActinomyces neuii (2 genomes, 1053 marker genes, 132 marker sets)\n-Actinomyces odontolyticus\tActinomyces odontolyticus (2 genomes, 1061 marker genes, 179 marker sets)\n-Aeromonas hydrophila\tAeromonas hydrophila (3 genomes, 1847 marker genes, 312 marker sets)\n-Aeromonas veronii\tAeromonas veronii (6 genomes, 1752 marker genes, 329 marker sets)\n-Aggregatibacter actinomycetemcomitans\tAggregatibacter actinomycetemcomitans (10 genomes, 1164 marker genes, 217 marker sets)\n-Agrobacterium tumefaciens\tAgrobacterium tumefaciens (2 genomes, 1574 marker genes, 278 marker sets)\n-Alicycliphilus denitrificans\tAlicycliphilus denitrificans (2 genomes, 1650 marker genes, 258 marker sets)\n-Alicyclobacillus acidocaldarius\tAlicyclobacillus acidocaldarius (2 genomes, 1329 marker genes, 157 marker sets)\n-Alloscardovia omnicolens\tAlloscardovia omnicolens (2 genomes, 950 marker genes, 116 marker sets)\n-Alteromonas macleodii\tAlteromonas macleodii (4 genomes, 1539 marker genes, 274 marker sets)\n-Amycolatopsis mediterranei\tAmycolatopsis mediterranei (3 genomes, 1557 marker genes, 526 marker sets)\n-Anabaena circinalis\tAnabaena circinalis (2 genomes, 1357 marker genes, 362 marker sets)\n-Anaerococcus prevotii\tAnaerococcus prevotii (2 genomes, 900 marker genes, 143 marker sets)\n-Anaeromyxobacter dehalogenans\tAnaeromyxobacter dehalogenans (2 genomes, 1441 marker genes, 335 marker sets)\n-Anoxybacillus flavithermus\tAnoxybacillus flavithermus (2 genomes, 1366 marker genes, 163 marker sets)\n-Archaeoglobus fulgidus\tArchaeoglobus fulgidus (2 genomes, 975 marker genes, 111 marker sets)\n-Arcobacter butzleri\tArcobacter butzleri (4 genomes, 1067 marker genes, 144 marker sets)\n-Arthrobacter nicotinovorans\tArthrobacter nicotinovorans (2 genomes, 1382 marker genes, 287 marker sets)\n-Arthrospira platensis\tArthrospira platensis (2 genomes, 1432 marker genes, 419 marker sets)\n-Atopobium vaginae\tAtopobium vaginae (2 genomes, 714 mark'..b'es, 778 marker genes, 149 marker sets)\n-Sulfolobus solfataricus\tSulfolobus solfataricus (2 genomes, 822 marker genes, 116 marker sets)\n-Sutterella wadsworthensis\tSutterella wadsworthensis (3 genomes, 935 marker genes, 232 marker sets)\n-Synechococcus elongatus\tSynechococcus elongatus (2 genomes, 1468 marker genes, 121 marker sets)\n-Taylorella asinigenitalis\tTaylorella asinigenitalis (2 genomes, 1125 marker genes, 58 marker sets)\n-Taylorella equigenitalis\tTaylorella equigenitalis (2 genomes, 1154 marker genes, 53 marker sets)\n-Teredinibacter turnerae\tTeredinibacter turnerae (8 genomes, 1640 marker genes, 312 marker sets)\n-Thauera linaloolentis\tThauera linaloolentis (2 genomes, 1773 marker genes, 294 marker sets)\n-Thermacetogenium phaeum\tThermacetogenium phaeum (2 genomes, 1344 marker genes, 157 marker sets)\n-Thermoanaerobacterium thermosaccharolyticum\tThermoanaerobacterium thermosaccharolyticum (2 genomes, 1317 marker genes, 136 marker sets)\n-Thermobifida fusca\tThermobifida fusca (2 genomes, 1421 marker genes, 225 marker sets)\n-Thermus oshimai\tThermus oshimai (2 genomes, 1196 marker genes, 112 marker sets)\n-Thermus scotoductus\tThermus scotoductus (2 genomes, 1098 marker genes, 162 marker sets)\n-Thermus thermophilus\tThermus thermophilus (4 genomes, 1100 marker genes, 123 marker sets)\n-Thioalkalivibrio thiocyanoxidans\tThioalkalivibrio thiocyanoxidans (2 genomes, 1159 marker genes, 330 marker sets)\n-Thiobacillus denitrificans\tThiobacillus denitrificans (2 genomes, 1290 marker genes, 203 marker sets)\n-Treponema denticola\tTreponema denticola (9 genomes, 954 marker genes, 221 marker sets)\n-Treponema pallidum\tTreponema pallidum (3 genomes, 717 marker genes, 44 marker sets)\n-Treponema vincentii\tTreponema vincentii (2 genomes, 946 marker genes, 178 marker sets)\n-Ureaplasma parvum\tUreaplasma parvum (5 genomes, 420 marker genes, 35 marker sets)\n-Ureaplasma urealyticum\tUreaplasma urealyticum (10 genomes, 386 marker genes, 50 marker sets)\n-Variovorax paradoxus\tVariovorax paradoxus (5 genomes, 1314 marker genes, 368 marker sets)\n-Veillonella atypica\tVeillonella atypica (3 genomes, 1145 marker genes, 136 marker sets)\n-Veillonella parvula\tVeillonella parvula (2 genomes, 1174 marker genes, 97 marker sets)\n-Vibrio alginolyticus\tVibrio alginolyticus (5 genomes, 1283 marker genes, 392 marker sets)\n-Vibrio cholerae\tVibrio cholerae (20 genomes, 1729 marker genes, 348 marker sets)\n-Vibrio fischeri\tVibrio fischeri (2 genomes, 1814 marker genes, 227 marker sets)\n-Vibrio harveyi\tVibrio harveyi (3 genomes, 1674 marker genes, 373 marker sets)\n-Vibrio mimicus\tVibrio mimicus (2 genomes, 1752 marker genes, 276 marker sets)\n-Vibrio parahaemolyticus\tVibrio parahaemolyticus (12 genomes, 1733 marker genes, 363 marker sets)\n-Vibrio splendidus\tVibrio splendidus (2 genomes, 1757 marker genes, 310 marker sets)\n-Vibrio vulnificus\tVibrio vulnificus (5 genomes, 1802 marker genes, 386 marker sets)\n-Wigglesworthia glossinidia\tWigglesworthia glossinidia (2 genomes, 679 marker genes, 9 marker sets)\n-Wohlfahrtiimonas chitiniclastica\tWohlfahrtiimonas chitiniclastica (2 genomes, 1335 marker genes, 78 marker sets)\n-Wolbachia endosymbiont of Culex quinquefasciatus\tWolbachia endosymbiont of Culex quinquefasciatus (2 genomes, 747 marker genes, 56 marker sets)\n-Xanthomonas axonopodis\tXanthomonas axonopodis (5 genomes, 1627 marker genes, 365 marker sets)\n-Xanthomonas campestris\tXanthomonas campestris (5 genomes, 1623 marker genes, 336 marker sets)\n-Xanthomonas oryzae\tXanthomonas oryzae (3 genomes, 1627 marker genes, 339 marker sets)\n-Xylella fastidiosa\tXylella fastidiosa (10 genomes, 1207 marker genes, 178 marker sets)\n-Yersinia enterocolitica\tYersinia enterocolitica (5 genomes, 1868 marker genes, 316 marker sets)\n-Yersinia pestis\tYersinia pestis (20 genomes, 1683 marker genes, 330 marker sets)\n-Yersinia pseudotuberculosis\tYersinia pseudotuberculosis (4 genomes, 1975 marker genes, 263 marker sets)\n-Zymomonas mobilis\tZymomonas mobilis (3 genomes, 1142 marker genes, 133 marker sets)\n' |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,30 +0,0 @@ -<tables> - <table name="life_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/life.loc" /> - </table> - <table name="domain_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/domain.loc" /> - </table> - <table name="phylum_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/phylum.loc" /> - </table> - <table name="order_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/order.loc" /> - </table> - <table name="family_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/family.loc" /> - </table> - <table name="genus_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/genus.loc" /> - </table> - <table name="species_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/species.loc" /> - </table> -</tables> \ No newline at end of file |
| b |
| diff -r 0ea86ba426e1 -r 98731fd340c5 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue Jun 17 12:57:06 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<tables> - <table name="life_taxons" comment_char="#"> - <columns>value, name</columns> - <file path="${__HERE__}/test-data/life.loc" /> - </table> -</tables> \ No newline at end of file |