Mercurial > repos > iuc > busco
comparison macros.xml @ 7:4048d82f0c88 draft
"planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c"
| author | iuc |
|---|---|
| date | Mon, 17 Aug 2020 06:50:18 -0400 |
| parents | |
| children | 602fb8e63aa7 |
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| 6:1e62c28ba91d | 7:4048d82f0c88 |
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| 1 <?xml version="1.0"?> | |
| 2 <macros> | |
| 3 <token name="@TOOL_VERSION@">4.1.2</token> | |
| 4 | |
| 5 <xml name="citations"> | |
| 6 <citations> | |
| 7 <citation type="doi">10.1093/bioinformatics/btv351</citation> | |
| 8 </citations> | |
| 9 </xml> | |
| 10 | |
| 11 <xml name="augustus_species"> | |
| 12 <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) --> | |
| 13 <option value="human">Homo sapiens</option> | |
| 14 <option value="fly">Drosophila melanogaster</option> | |
| 15 <option value="arabidopsis">Arabidopsis thaliana</option> | |
| 16 <option value="brugia ">Brugia malayi</option> | |
| 17 <option value="aedes">Aedes aegypti</option> | |
| 18 <option value="tribolium2012">Tribolium castaneum</option> | |
| 19 <option value="schistosoma">Schistosoma mansoni</option> | |
| 20 <option value="tetrahymena">Tetrahymena thermophila</option> | |
| 21 <option value="galdieria">Galdieria sulphuraria</option> | |
| 22 <option value="maize">Zea mays</option> | |
| 23 <option value="toxoplasma">Toxoplasma gondii</option> | |
| 24 <option value="caenorhabditis ">Caenorhabditis elegans</option> | |
| 25 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> | |
| 26 <option value="aspergillus_nidulans ">Aspergillus nidulans</option> | |
| 27 <option value="aspergillus_oryzae ">Aspergillus oryzae</option> | |
| 28 <option value="aspergillus_terreus">Aspergillus terreus</option> | |
| 29 <option value="botrytis_cinerea ">Botrytis cinerea</option> | |
| 30 <option value="candida_albicans ">Candida albicans</option> | |
| 31 <option value="candida_guilliermondii ">Candida guilliermondii</option> | |
| 32 <option value="candida_tropicalis ">Candida tropicalis</option> | |
| 33 <option value="chaetomium_globosum">Chaetomium globosum</option> | |
| 34 <option value="coccidioides_immitis">Coccidioides immitis</option> | |
| 35 <option value="coprinus">Coprinus cinereus</option> | |
| 36 <option value="coprinus_cinereus">Coprinus cinereus</option> | |
| 37 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> | |
| 38 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> | |
| 39 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> | |
| 40 <option value="cryptococcus">Cryptococcus neoformans</option> | |
| 41 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> | |
| 42 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> | |
| 43 <option value="eremothecium_gossypii">Eremothecium gossypii</option> | |
| 44 <option value="fusarium_graminearum ">Fusarium graminearum</option> | |
| 45 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> | |
| 46 <option value="histoplasma">Histoplasma capsulatum</option> | |
| 47 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> | |
| 48 <option value="laccaria_bicolor ">Laccaria bicolor</option> | |
| 49 <option value="lamprey">Petromyzon marinus</option> | |
| 50 <option value="leishmania_tarentolae">Leishmania tarentolae</option> | |
| 51 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> | |
| 52 <option value="magnaporthe_grisea ">Magnaporthe grisea</option> | |
| 53 <option value="neurospora_crassa">Neurospora crassa</option> | |
| 54 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> | |
| 55 <option value="pichia_stipitis">Pichia stipitis</option> | |
| 56 <option value="rhizopus_oryzae">Rhizopus oryzae</option> | |
| 57 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> | |
| 58 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> | |
| 59 <option value="saccharomyces">Saccharomyces cerevisiae</option> | |
| 60 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> | |
| 61 <option value="trichinella">Trichinella spiralis</option> | |
| 62 <option value="ustilago_maydis">Ustilago maydis</option> | |
| 63 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> | |
| 64 <option value="nasonia">Nasonia vitripennis</option> | |
| 65 <option value="tomato">Solanum lycopersicum</option> | |
| 66 <option value="chlamydomonas">Chlamydomonas reinhardtii</option> | |
| 67 <option value="amphimedon">Amphimedon queenslandica</option> | |
| 68 <option value="pneumocystis">Pneumocystis jirovecii</option> | |
| 69 <option value="chicken">Gallus gallus domesticus (chicken)</option> | |
| 70 <option value="cacao">Theobroma cacao (cacao)</option> | |
| 71 <option value="heliconius_melpomene1">Heliconius melpomene</option> | |
| 72 <option value="xenoturbella">Xenoturbella</option> | |
| 73 <option value="E_coli_K12">E coli K12</option> | |
| 74 <option value="c_elegans_trsk">c elegans trsk</option> | |
| 75 <option value="camponotus_floridanus">Camponotus floridanus</option> | |
| 76 <option value="coyote_tobacco">Coyote tobacco</option> | |
| 77 <option value="s_aureus">Staphylococcus aureus</option> | |
| 78 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> | |
| 79 <option value="wheat">wheat</option> | |
| 80 <option value="zebrafish">Danio rerio</option> | |
| 81 <option value="anidulans">Aspergillus nidulans</option> | |
| 82 <option value="bombus_impatiens1">Bombus impatiens1</option> | |
| 83 <option value="bombus_terrestris2">Bombus terrestris2</option> | |
| 84 <option value="botrytis_cinerea">Botrytis cinerea</option> | |
| 85 <option value="brugia_malayi">Brugia malayi</option> | |
| 86 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> | |
| 87 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option> | |
| 88 <option value="culex_pipiens">Culex pipiens</option> | |
| 89 <option value="elephant_shark">Callorhinchus milii</option> | |
| 90 <option value="honeybee1">Apis mellifera</option> | |
| 91 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> | |
| 92 <option value="pea_aphid">Acyrthosiphon pisum</option> | |
| 93 <option value="rhodnius_prolixus">Rhodnius prolixus</option> | |
| 94 <option value="ustilago_maydis">Ustilago maydis</option> | |
| 95 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> | |
| 96 <option value="verticillium_longisporum1">Verticillium longisporum1</option> | |
| 97 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> | |
| 98 <option value="adorsata">adorsata</option> | |
| 99 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> | |
| 100 <option value="maker2_athal1">maker2_athal1</option> | |
| 101 <option value="maker2_c_elegans1">maker2_c_elegans1</option> | |
| 102 <option value="maker2_dmel1">maker2_dmel1</option> | |
| 103 <option value="maker2_spomb1">maker2_spomb1</option> | |
| 104 <option value="parasteatoda">parasteatoda</option> | |
| 105 <option value="rice">rice</option> | |
| 106 <option value="schistosoma2">schistosoma2</option> | |
| 107 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> | |
| 108 </xml> | |
| 109 | |
| 110 <xml name="lineages"> | |
| 111 <option value="acidobacteria_odb10">Acidobacteria</option> | |
| 112 <option value="aconoidasida_odb10">Aconoidasida</option> | |
| 113 <option value="actinobacteria_class_odb10">Actinobacteria class</option> | |
| 114 <option value="actinobacteria_phylum_odb10">Actinobacteria phylum</option> | |
| 115 <option value="actinopterygii_odb10">Actinopterygii</option> | |
| 116 <option value="agaricales_odb10">Agaricales</option> | |
| 117 <option value="agaricomycetes_odb10">Agaricomycetes</option> | |
| 118 <option value="alphaproteobacteria_odb10">Alphaproteobacteria</option> | |
| 119 <option value="alteromonadales_odb10">Alteromonadales</option> | |
| 120 <option value="alveolata_odb10">Alveolata</option> | |
| 121 <option value="apicomplexa_odb10">Apicomplexa</option> | |
| 122 <option value="aquificae_odb10">Aquificae</option> | |
| 123 <option value="arachnida_odb10">Arachnida</option> | |
| 124 <option value="archaea_odb10">Archaea</option> | |
| 125 <option value="arthropoda_odb10">Arthropoda</option> | |
| 126 <option value="ascomycota_odb10">Ascomycota</option> | |
| 127 <option value="aves_odb10">Aves</option> | |
| 128 <option value="bacillales_odb10">Bacillales</option> | |
| 129 <option value="bacilli_odb10">Bacilli</option> | |
| 130 <option value="bacteria_odb10">Bacteria</option> | |
| 131 <option value="bacteroidales_odb10">Bacteroidales</option> | |
| 132 <option value="bacteroidetes-chlorobi_group_odb10">Bacteroidetes-chlorobi group</option> | |
| 133 <option value="bacteroidetes_odb10">Bacteroidetes</option> | |
| 134 <option value="bacteroidia_odb10">Bacteroidia</option> | |
| 135 <option value="basidiomycota_odb10">Basidiomycota</option> | |
| 136 <option value="betaproteobacteria_odb10">Betaproteobacteria</option> | |
| 137 <option value="boletales_odb10">Boletales</option> | |
| 138 <option value="brassicales_odb10">Brassicales</option> | |
| 139 <option value="burkholderiales_odb10">Burkholderiales</option> | |
| 140 <option value="campylobacterales_odb10">Campylobacterales</option> | |
| 141 <option value="capnodiales_odb10">Capnodiales</option> | |
| 142 <option value="carnivora_odb10">Carnivora</option> | |
| 143 <option value="cellvibrionales_odb10">Cellvibrionales</option> | |
| 144 <option value="cetartiodactyla_odb10">Cetartiodactyla</option> | |
| 145 <option value="chaetothyriales_odb10">Chaetothyriales</option> | |
| 146 <option value="chlamydiae_odb10">Chlamydiae</option> | |
| 147 <option value="chlorobi_odb10">Chlorobi</option> | |
| 148 <option value="chloroflexi_odb10">Chloroflexi</option> | |
| 149 <option value="chlorophyta_odb10">Chlorophyta</option> | |
| 150 <option value="chromatiales_odb10">Chromatiales</option> | |
| 151 <option value="chroococcales_odb10">Chroococcales</option> | |
| 152 <option value="clostridia_odb10">Clostridia</option> | |
| 153 <option value="clostridiales_odb10">Clostridiales</option> | |
| 154 <option value="coccidia_odb10">Coccidia</option> | |
| 155 <option value="coriobacteriales_odb10">Coriobacteriales</option> | |
| 156 <option value="coriobacteriia_odb10">Coriobacteriia</option> | |
| 157 <option value="corynebacteriales_odb10">Corynebacteriales</option> | |
| 158 <option value="cyanobacteria_odb10">Cyanobacteria</option> | |
| 159 <option value="cyprinodontiformes_odb10">Cyprinodontiformes</option> | |
| 160 <option value="cytophagales_odb10">Cytophagales</option> | |
| 161 <option value="cytophagia_odb10">Cytophagia</option> | |
| 162 <option value="delta-epsilon-subdivisions_odb10">Delta-epsilon-subdivisions</option> | |
| 163 <option value="deltaproteobacteria_odb10">Deltaproteobacteria</option> | |
| 164 <option value="desulfobacterales_odb10">Desulfobacterales</option> | |
| 165 <option value="desulfovibrionales_odb10">Desulfovibrionales</option> | |
| 166 <option value="desulfurococcales_odb10">Desulfurococcales</option> | |
| 167 <option value="desulfuromonadales_odb10">Desulfuromonadales</option> | |
| 168 <option value="diptera_odb10">Diptera</option> | |
| 169 <option value="dothideomycetes_odb10">Dothideomycetes</option> | |
| 170 <option value="embryophyta_odb10">Embryophyta</option> | |
| 171 <option value="endopterygota_odb10">Endopterygota</option> | |
| 172 <option value="enterobacterales_odb10">Enterobacterales</option> | |
| 173 <option value="entomoplasmatales_odb10">Entomoplasmatales</option> | |
| 174 <option value="epsilonproteobacteria_odb10">Epsilonproteobacteria</option> | |
| 175 <option value="euarchontoglires_odb10">Euarchontoglires</option> | |
| 176 <option value="eudicots_odb10">Eudicots</option> | |
| 177 <option value="euglenozoa_odb10">Euglenozoa</option> | |
| 178 <option value="eukaryota_odb10">Eukaryota</option> | |
| 179 <option value="eurotiales_odb10">Eurotiales</option> | |
| 180 <option value="eurotiomycetes_odb10">Eurotiomycetes</option> | |
| 181 <option value="euryarchaeota_odb10">Euryarchaeota</option> | |
| 182 <option value="eutheria_odb10">Eutheria</option> | |
| 183 <option value="fabales_odb10">Fabales</option> | |
| 184 <option value="firmicutes_odb10">Firmicutes</option> | |
| 185 <option value="flavobacteriales_odb10">Flavobacteriales</option> | |
| 186 <option value="flavobacteriia_odb10">Flavobacteriia</option> | |
| 187 <option value="fungi_odb10">Fungi</option> | |
| 188 <option value="fusobacteria_odb10">Fusobacteria</option> | |
| 189 <option value="fusobacteriales_odb10">Fusobacteriales</option> | |
| 190 <option value="gammaproteobacteria_odb10">Gammaproteobacteria</option> | |
| 191 <option value="glires_odb10">Glires</option> | |
| 192 <option value="glomerellales_odb10">Glomerellales</option> | |
| 193 <option value="halobacteria_odb10">Halobacteria</option> | |
| 194 <option value="halobacteriales_odb10">Halobacteriales</option> | |
| 195 <option value="haloferacales_odb10">Haloferacales</option> | |
| 196 <option value="helotiales_odb10">Helotiales</option> | |
| 197 <option value="hemiptera_odb10">Hemiptera</option> | |
| 198 <option value="hymenoptera_odb10">Hymenoptera</option> | |
| 199 <option value="hypocreales_odb10">Hypocreales</option> | |
| 200 <option value="insecta_odb10">Insecta</option> | |
| 201 <option value="lactobacillales_odb10">Lactobacillales</option> | |
| 202 <option value="laurasiatheria_odb10">Laurasiatheria</option> | |
| 203 <option value="legionellales_odb10">Legionellales</option> | |
| 204 <option value="leotiomycetes_odb10">Leotiomycetes</option> | |
| 205 <option value="lepidoptera_odb10">Lepidoptera</option> | |
| 206 <option value="liliopsida_odb10">Liliopsida</option> | |
| 207 <option value="mammalia_odb10">Mammalia</option> | |
| 208 <option value="metazoa_odb10">Metazoa</option> | |
| 209 <option value="methanobacteria_odb10">Methanobacteria</option> | |
| 210 <option value="methanococcales_odb10">Methanococcales</option> | |
| 211 <option value="methanomicrobia_odb10">Methanomicrobia</option> | |
| 212 <option value="methanomicrobiales_odb10">Methanomicrobiales</option> | |
| 213 <option value="micrococcales_odb10">Micrococcales</option> | |
| 214 <option value="microsporidia_odb10">Microsporidia</option> | |
| 215 <option value="mollicutes_odb10">Mollicutes</option> | |
| 216 <option value="mollusca_odb10">Mollusca</option> | |
| 217 <option value="mucorales_odb10">Mucorales</option> | |
| 218 <option value="mucoromycota_odb10">Mucoromycota</option> | |
| 219 <option value="mycoplasmatales_odb10">Mycoplasmatales</option> | |
| 220 <option value="natrialbales_odb10">Natrialbales</option> | |
| 221 <option value="neisseriales_odb10">Neisseriales</option> | |
| 222 <option value="nematoda_odb10">Nematoda</option> | |
| 223 <option value="nitrosomonadales_odb10">Nitrosomonadales</option> | |
| 224 <option value="nostocales_odb10">Nostocales</option> | |
| 225 <option value="oceanospirillales_odb10">Oceanospirillales</option> | |
| 226 <option value="onygenales_odb10">Onygenales</option> | |
| 227 <option value="oscillatoriales_odb10">Oscillatoriales</option> | |
| 228 <option value="passeriformes_odb10">Passeriformes</option> | |
| 229 <option value="pasteurellales_odb10">Pasteurellales</option> | |
| 230 <option value="planctomycetes_odb10">Planctomycetes</option> | |
| 231 <option value="plasmodium_odb10">Plasmodium</option> | |
| 232 <option value="pleosporales_odb10">Pleosporales</option> | |
| 233 <option value="poales_odb10">Poales</option> | |
| 234 <option value="polyporales_odb10">Polyporales</option> | |
| 235 <option value="primates_odb10">Primates</option> | |
| 236 <option value="propionibacteriales_odb10">Propionibacteriales</option> | |
| 237 <option value="proteobacteria_odb10">Proteobacteria</option> | |
| 238 <option value="pseudomonadales_odb10">Pseudomonadales</option> | |
| 239 <option value="rhizobiales_odb10">Rhizobiales</option> | |
| 240 <option value="rhizobium-agrobacterium_group_odb10">Rhizobium-agrobacterium group</option> | |
| 241 <option value="rhodobacterales_odb10">Rhodobacterales</option> | |
| 242 <option value="rhodospirillales_odb10">Rhodospirillales</option> | |
| 243 <option value="rickettsiales_odb10">Rickettsiales</option> | |
| 244 <option value="saccharomycetes_odb10">Saccharomycetes</option> | |
| 245 <option value="sauropsida_odb10">Sauropsida</option> | |
| 246 <option value="selenomonadales_odb10">Selenomonadales</option> | |
| 247 <option value="solanales_odb10">Solanales</option> | |
| 248 <option value="sordariomycetes_odb10">Sordariomycetes</option> | |
| 249 <option value="sphingobacteriia_odb10">Sphingobacteriia</option> | |
| 250 <option value="sphingomonadales_odb10">Sphingomonadales</option> | |
| 251 <option value="spirochaetales_odb10">Spirochaetales</option> | |
| 252 <option value="spirochaetes_odb10">Spirochaetes</option> | |
| 253 <option value="spirochaetia_odb10">Spirochaetia</option> | |
| 254 <option value="stramenopiles_odb10">Stramenopiles</option> | |
| 255 <option value="streptomycetales_odb10">Streptomycetales</option> | |
| 256 <option value="streptosporangiales_odb10">Streptosporangiales</option> | |
| 257 <option value="sulfolobales_odb10">Sulfolobales</option> | |
| 258 <option value="synechococcales_odb10">Synechococcales</option> | |
| 259 <option value="synergistetes_odb10">Synergistetes</option> | |
| 260 <option value="tenericutes_odb10">Tenericutes</option> | |
| 261 <option value="tetrapoda_odb10">Tetrapoda</option> | |
| 262 <option value="thaumarchaeota_odb10">Thaumarchaeota</option> | |
| 263 <option value="thermoanaerobacterales_odb10">Thermoanaerobacterales</option> | |
| 264 <option value="thermoplasmata_odb10">Thermoplasmata</option> | |
| 265 <option value="thermoproteales_odb10">Thermoproteales</option> | |
| 266 <option value="thermoprotei_odb10">Thermoprotei</option> | |
| 267 <option value="thermotogae_odb10">Thermotogae</option> | |
| 268 <option value="thiotrichales_odb10">Thiotrichales</option> | |
| 269 <option value="tissierellales_odb10">Tissierellales</option> | |
| 270 <option value="tissierellia_odb10">Tissierellia</option> | |
| 271 <option value="tremellomycetes_odb10">Tremellomycetes</option> | |
| 272 <option value="verrucomicrobia_odb10">Verrucomicrobia</option> | |
| 273 <option value="vertebrata_odb10">Vertebrata</option> | |
| 274 <option value="vibrionales_odb10">Vibrionales</option> | |
| 275 <option value="viridiplantae_odb10">Viridiplantae</option> | |
| 276 <option value="xanthomonadales_odb10">Xanthomonadales</option> | |
| 277 </xml> | |
| 278 </macros> |