Mercurial > repos > iuc > funannotate_annotate
comparison macros.xml @ 0:a5baa4ff168d draft
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
| author | iuc |
|---|---|
| date | Mon, 04 Oct 2021 19:39:38 +0000 |
| parents | |
| children | 78407487f758 |
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| -1:000000000000 | 0:a5baa4ff168d |
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| 1 <?xml version="1.0"?> | |
| 2 <macros> | |
| 3 <token name="@TOOL_VERSION@">1.8.9</token> | |
| 4 <token name="@VERSION_SUFFIX@">1</token> | |
| 5 | |
| 6 <xml name="requirements"> | |
| 7 <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement> | |
| 8 </xml> | |
| 9 | |
| 10 <xml name="citations"> | |
| 11 <citations> | |
| 12 <citation type="doi">10.5281/zenodo.4054262</citation> | |
| 13 </citations> | |
| 14 </xml> | |
| 15 | |
| 16 <xml name="augustus_species"> | |
| 17 <!-- list generated from a Funannotate database directory, listing trained_species/* --> | |
| 18 <option value="adorsata">adorsata</option> | |
| 19 <option value="aedes">aedes</option> | |
| 20 <option value="amphimedon">amphimedon</option> | |
| 21 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> | |
| 22 <option value="anidulans">anidulans</option> | |
| 23 <option value="arabidopsis">arabidopsis</option> | |
| 24 <option value="aspergillus_fumigatus">aspergillus_fumigatus</option> | |
| 25 <option value="aspergillus_nidulans">aspergillus_nidulans</option> | |
| 26 <option value="aspergillus_oryzae">aspergillus_oryzae</option> | |
| 27 <option value="aspergillus_terreus">aspergillus_terreus</option> | |
| 28 <option value="bombus_impatiens1">bombus_impatiens1</option> | |
| 29 <option value="bombus_terrestris2">bombus_terrestris2</option> | |
| 30 <option value="botrytis_cinerea">botrytis_cinerea</option> | |
| 31 <option value="b_pseudomallei">b_pseudomallei</option> | |
| 32 <option value="brugia">brugia</option> | |
| 33 <option value="cacao">cacao</option> | |
| 34 <option value="caenorhabditis">caenorhabditis</option> | |
| 35 <option value="camponotus_floridanus">camponotus_floridanus</option> | |
| 36 <option value="candida_albicans">candida_albicans</option> | |
| 37 <option value="candida_guilliermondii">candida_guilliermondii</option> | |
| 38 <option value="candida_tropicalis">candida_tropicalis</option> | |
| 39 <option value="c_elegans_trsk">c_elegans_trsk</option> | |
| 40 <option value="chaetomium_globosum">chaetomium_globosum</option> | |
| 41 <option value="chicken">chicken</option> | |
| 42 <option value="chiloscyllium">chiloscyllium</option> | |
| 43 <option value="chlamy2011">chlamy2011</option> | |
| 44 <option value="chlamydomonas">chlamydomonas</option> | |
| 45 <option value="chlorella">chlorella</option> | |
| 46 <option value="ciona">ciona</option> | |
| 47 <option value="coccidioides_immitis">coccidioides_immitis</option> | |
| 48 <option value="Conidiobolus_coronatus">Conidiobolus_coronatus</option> | |
| 49 <option value="coprinus">coprinus</option> | |
| 50 <option value="coprinus_cinereus">coprinus_cinereus</option> | |
| 51 <option value="coyote_tobacco">coyote_tobacco</option> | |
| 52 <option value="cryptococcus">cryptococcus</option> | |
| 53 <option value="cryptococcus_neoformans_gattii">cryptococcus_neoformans_gattii</option> | |
| 54 <option value="cryptococcus_neoformans_neoformans_B">cryptococcus_neoformans_neoformans_B</option> | |
| 55 <option value="cryptococcus_neoformans_neoformans_JEC21">cryptococcus_neoformans_neoformans_JEC21</option> | |
| 56 <option value="culex">culex</option> | |
| 57 <option value="debaryomyces_hansenii">debaryomyces_hansenii</option> | |
| 58 <option value="E_coli_K12">E_coli_K12</option> | |
| 59 <option value="elephant_shark">elephant_shark</option> | |
| 60 <option value="encephalitozoon_cuniculi_GB">encephalitozoon_cuniculi_GB</option> | |
| 61 <option value="eremothecium_gossypii">eremothecium_gossypii</option> | |
| 62 <option value="fly">fly</option> | |
| 63 <option value="fly_exp">fly_exp</option> | |
| 64 <option value="fusarium">fusarium</option> | |
| 65 <option value="fusarium_graminearum">fusarium_graminearum</option> | |
| 66 <option value="galdieria">galdieria</option> | |
| 67 <option value="generic">generic</option> | |
| 68 <option value="heliconius_melpomene1">heliconius_melpomene1</option> | |
| 69 <option value="histoplasma">histoplasma</option> | |
| 70 <option value="histoplasma_capsulatum">histoplasma_capsulatum</option> | |
| 71 <option value="honeybee1">honeybee1</option> | |
| 72 <option value="human">human</option> | |
| 73 <option value="japaneselamprey">japaneselamprey</option> | |
| 74 <option value="kluyveromyces_lactis">kluyveromyces_lactis</option> | |
| 75 <option value="laccaria_bicolor">laccaria_bicolor</option> | |
| 76 <option value="leishmania_tarentolae">leishmania_tarentolae</option> | |
| 77 <option value="lodderomyces_elongisporus">lodderomyces_elongisporus</option> | |
| 78 <option value="magnaporthe_grisea">magnaporthe_grisea</option> | |
| 79 <option value="maize">maize</option> | |
| 80 <option value="maize5">maize5</option> | |
| 81 <option value="mnemiopsis_leidyi">mnemiopsis_leidyi</option> | |
| 82 <option value="nasonia">nasonia</option> | |
| 83 <option value="nematostella_vectensis">nematostella_vectensis</option> | |
| 84 <option value="neurospora">neurospora</option> | |
| 85 <option value="neurospora_crassa">neurospora_crassa</option> | |
| 86 <option value="parasteatoda">parasteatoda</option> | |
| 87 <option value="pchrysosporium">pchrysosporium</option> | |
| 88 <option value="pea_aphid">pea_aphid</option> | |
| 89 <option value="pfalciparum">pfalciparum</option> | |
| 90 <option value="phanerochaete_chrysosporium">phanerochaete_chrysosporium</option> | |
| 91 <option value="pichia_stipitis">pichia_stipitis</option> | |
| 92 <option value="pisaster">pisaster</option> | |
| 93 <option value="pneumocystis">pneumocystis</option> | |
| 94 <option value="rhincodon">rhincodon</option> | |
| 95 <option value="rhizopus_oryzae">rhizopus_oryzae</option> | |
| 96 <option value="rhodnius">rhodnius</option> | |
| 97 <option value="rice">rice</option> | |
| 98 <option value="saccharomyces">saccharomyces</option> | |
| 99 <option value="saccharomyces_cerevisiae_rm11-1a_1">saccharomyces_cerevisiae_rm11-1a_1</option> | |
| 100 <option value="saccharomyces_cerevisiae_S288C">saccharomyces_cerevisiae_S288C</option> | |
| 101 <option value="s_aureus">s_aureus</option> | |
| 102 <option value="schistosoma">schistosoma</option> | |
| 103 <option value="schistosoma2">schistosoma2</option> | |
| 104 <option value="schizosaccharomyces_pombe">schizosaccharomyces_pombe</option> | |
| 105 <option value="scyliorhinus">scyliorhinus</option> | |
| 106 <option value="sealamprey">sealamprey</option> | |
| 107 <option value="s_pneumoniae">s_pneumoniae</option> | |
| 108 <option value="strongylocentrotus_purpuratus">strongylocentrotus_purpuratus</option> | |
| 109 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> | |
| 110 <option value="template_prokaryotic">template_prokaryotic</option> | |
| 111 <option value="tetrahymena">tetrahymena</option> | |
| 112 <option value="thermoanaerobacter_tengcongensis">thermoanaerobacter_tengcongensis</option> | |
| 113 <option value="tomato">tomato</option> | |
| 114 <option value="toxoplasma">toxoplasma</option> | |
| 115 <option value="tribolium2012">tribolium2012</option> | |
| 116 <option value="trichinella">trichinella</option> | |
| 117 <option value="ustilago">ustilago</option> | |
| 118 <option value="ustilago_maydis">ustilago_maydis</option> | |
| 119 <option value="verticillium_albo_atrum1">verticillium_albo_atrum1</option> | |
| 120 <option value="verticillium_longisporum1">verticillium_longisporum1</option> | |
| 121 <option value="volvox">volvox</option> | |
| 122 <option value="wheat">wheat</option> | |
| 123 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> | |
| 124 <option value="yarrowia_lipolytica">yarrowia_lipolytica</option> | |
| 125 <option value="zebrafish">zebrafish</option> | |
| 126 </xml> | |
| 127 | |
| 128 <xml name="busco_species"> | |
| 129 <!-- list generated from a Funannotate database directory, with the "funannotate database -show-buscos command" --> | |
| 130 <option value="eukaryota">eukaryota</option> | |
| 131 <option value="metazoa">metazoa</option> | |
| 132 <option value="nematoda">nematoda</option> | |
| 133 <option value="arthropoda">arthropoda</option> | |
| 134 <option value="insecta">insecta</option> | |
| 135 <option value="endopterygota">endopterygota</option> | |
| 136 <option value="hymenoptera">hymenoptera</option> | |
| 137 <option value="diptera">diptera</option> | |
| 138 <option value="vertebrata">vertebrata</option> | |
| 139 <option value="actinopterygii">actinopterygii</option> | |
| 140 <option value="tetrapoda">tetrapoda</option> | |
| 141 <option value="aves">aves</option> | |
| 142 <option value="mammalia">mammalia</option> | |
| 143 <option value="euarchontoglires">euarchontoglires</option> | |
| 144 <option value="laurasiatheria">laurasiatheria</option> | |
| 145 <option value="fungi">fungi</option> | |
| 146 <option value="dikarya">dikarya</option> | |
| 147 <option value="ascomycota">ascomycota</option> | |
| 148 <option value="pezizomycotina">pezizomycotina</option> | |
| 149 <option value="eurotiomycetes">eurotiomycetes</option> | |
| 150 <option value="sordariomycetes">sordariomycetes</option> | |
| 151 <option value="saccharomycetes">saccharomycetes</option> | |
| 152 <option value="saccharomycetales">saccharomycetales</option> | |
| 153 <option value="basidiomycota">basidiomycota</option> | |
| 154 <option value="microsporidia">microsporidia</option> | |
| 155 <option value="embryophyta">embryophyta</option> | |
| 156 <option value="protists">protists</option> | |
| 157 <option value="alveolata_stramenophiles">alveolata_stramenophiles</option> | |
| 158 </xml> | |
| 159 </macros> |