annotate macros.xml @ 2:922ff4f431b3 draft

"planemo upload commit febca656bf539c044816abebfeef3c84adc4056e"

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.8.9</token>
    <token name="@VERSION_SUFFIX@">1</token>

    <xml name="requirements">
        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.4054262</citation>
        </citations>
    </xml>

    <xml name="augustus_species">
        <!-- list generated from a Funannotate database directory, listing trained_species/* -->
        <option value="adorsata">adorsata</option>
        <option value="aedes">aedes</option>
        <option value="amphimedon">amphimedon</option>
        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
        <option value="anidulans">anidulans</option>
        <option value="arabidopsis">arabidopsis</option>
        <option value="aspergillus_fumigatus">aspergillus_fumigatus</option>
        <option value="aspergillus_nidulans">aspergillus_nidulans</option>
        <option value="aspergillus_oryzae">aspergillus_oryzae</option>
        <option value="aspergillus_terreus">aspergillus_terreus</option>
        <option value="bombus_impatiens1">bombus_impatiens1</option>
        <option value="bombus_terrestris2">bombus_terrestris2</option>
        <option value="botrytis_cinerea">botrytis_cinerea</option>
        <option value="b_pseudomallei">b_pseudomallei</option>
        <option value="brugia">brugia</option>
        <option value="cacao">cacao</option>
        <option value="caenorhabditis">caenorhabditis</option>
        <option value="camponotus_floridanus">camponotus_floridanus</option>
        <option value="candida_albicans">candida_albicans</option>
        <option value="candida_guilliermondii">candida_guilliermondii</option>
        <option value="candida_tropicalis">candida_tropicalis</option>
        <option value="c_elegans_trsk">c_elegans_trsk</option>
        <option value="chaetomium_globosum">chaetomium_globosum</option>
        <option value="chicken">chicken</option>
        <option value="chiloscyllium">chiloscyllium</option>
        <option value="chlamy2011">chlamy2011</option>
        <option value="chlamydomonas">chlamydomonas</option>
        <option value="chlorella">chlorella</option>
        <option value="ciona">ciona</option>
        <option value="coccidioides_immitis">coccidioides_immitis</option>
        <option value="Conidiobolus_coronatus">Conidiobolus_coronatus</option>
        <option value="coprinus">coprinus</option>
        <option value="coprinus_cinereus">coprinus_cinereus</option>
        <option value="coyote_tobacco">coyote_tobacco</option>
        <option value="cryptococcus">cryptococcus</option>
        <option value="cryptococcus_neoformans_gattii">cryptococcus_neoformans_gattii</option>
        <option value="cryptococcus_neoformans_neoformans_B">cryptococcus_neoformans_neoformans_B</option>
        <option value="cryptococcus_neoformans_neoformans_JEC21">cryptococcus_neoformans_neoformans_JEC21</option>
        <option value="culex">culex</option>
        <option value="debaryomyces_hansenii">debaryomyces_hansenii</option>
        <option value="E_coli_K12">E_coli_K12</option>
        <option value="elephant_shark">elephant_shark</option>
        <option value="encephalitozoon_cuniculi_GB">encephalitozoon_cuniculi_GB</option>
        <option value="eremothecium_gossypii">eremothecium_gossypii</option>
        <option value="fly">fly</option>
        <option value="fly_exp">fly_exp</option>
        <option value="fusarium">fusarium</option>
        <option value="fusarium_graminearum">fusarium_graminearum</option>
        <option value="galdieria">galdieria</option>
        <option value="generic">generic</option>
        <option value="heliconius_melpomene1">heliconius_melpomene1</option>
        <option value="histoplasma">histoplasma</option>
        <option value="histoplasma_capsulatum">histoplasma_capsulatum</option>
        <option value="honeybee1">honeybee1</option>
        <option value="human">human</option>
        <option value="japaneselamprey">japaneselamprey</option>
        <option value="kluyveromyces_lactis">kluyveromyces_lactis</option>
        <option value="laccaria_bicolor">laccaria_bicolor</option>
        <option value="leishmania_tarentolae">leishmania_tarentolae</option>
        <option value="lodderomyces_elongisporus">lodderomyces_elongisporus</option>
        <option value="magnaporthe_grisea">magnaporthe_grisea</option>
        <option value="maize">maize</option>
        <option value="maize5">maize5</option>
        <option value="mnemiopsis_leidyi">mnemiopsis_leidyi</option>
        <option value="nasonia">nasonia</option>
        <option value="nematostella_vectensis">nematostella_vectensis</option>
        <option value="neurospora">neurospora</option>
        <option value="neurospora_crassa">neurospora_crassa</option>
        <option value="parasteatoda">parasteatoda</option>
        <option value="pchrysosporium">pchrysosporium</option>
        <option value="pea_aphid">pea_aphid</option>
        <option value="pfalciparum">pfalciparum</option>
        <option value="phanerochaete_chrysosporium">phanerochaete_chrysosporium</option>
        <option value="pichia_stipitis">pichia_stipitis</option>
        <option value="pisaster">pisaster</option>
        <option value="pneumocystis">pneumocystis</option>
        <option value="rhincodon">rhincodon</option>
        <option value="rhizopus_oryzae">rhizopus_oryzae</option>
        <option value="rhodnius">rhodnius</option>
        <option value="rice">rice</option>
        <option value="saccharomyces">saccharomyces</option>
        <option value="saccharomyces_cerevisiae_rm11-1a_1">saccharomyces_cerevisiae_rm11-1a_1</option>
        <option value="saccharomyces_cerevisiae_S288C">saccharomyces_cerevisiae_S288C</option>
        <option value="s_aureus">s_aureus</option>
        <option value="schistosoma">schistosoma</option>
        <option value="schistosoma2">schistosoma2</option>
        <option value="schizosaccharomyces_pombe">schizosaccharomyces_pombe</option>
        <option value="scyliorhinus">scyliorhinus</option>
        <option value="sealamprey">sealamprey</option>
        <option value="s_pneumoniae">s_pneumoniae</option>
        <option value="strongylocentrotus_purpuratus">strongylocentrotus_purpuratus</option>
        <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
        <option value="template_prokaryotic">template_prokaryotic</option>
        <option value="tetrahymena">tetrahymena</option>
        <option value="thermoanaerobacter_tengcongensis">thermoanaerobacter_tengcongensis</option>
        <option value="tomato">tomato</option>
        <option value="toxoplasma">toxoplasma</option>
        <option value="tribolium2012">tribolium2012</option>
        <option value="trichinella">trichinella</option>
        <option value="ustilago">ustilago</option>
        <option value="ustilago_maydis">ustilago_maydis</option>
        <option value="verticillium_albo_atrum1">verticillium_albo_atrum1</option>
        <option value="verticillium_longisporum1">verticillium_longisporum1</option>
        <option value="volvox">volvox</option>
        <option value="wheat">wheat</option>
        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
        <option value="yarrowia_lipolytica">yarrowia_lipolytica</option>
        <option value="zebrafish">zebrafish</option>
    </xml>

    <xml name="busco_species">
        <!-- list generated from a Funannotate database directory, with the "funannotate database -show-buscos command" -->
        <option value="eukaryota">eukaryota</option>
        <option value="metazoa">metazoa</option>
        <option value="nematoda">nematoda</option>
        <option value="arthropoda">arthropoda</option>
        <option value="insecta">insecta</option>
        <option value="endopterygota">endopterygota</option>
        <option value="hymenoptera">hymenoptera</option>
        <option value="diptera">diptera</option>
        <option value="vertebrata">vertebrata</option>
        <option value="actinopterygii">actinopterygii</option>
        <option value="tetrapoda">tetrapoda</option>
        <option value="aves">aves</option>
        <option value="mammalia">mammalia</option>
        <option value="euarchontoglires">euarchontoglires</option>
        <option value="laurasiatheria">laurasiatheria</option>
        <option value="fungi">fungi</option>
        <option value="dikarya">dikarya</option>
        <option value="ascomycota">ascomycota</option>
        <option value="pezizomycotina">pezizomycotina</option>
        <option value="eurotiomycetes">eurotiomycetes</option>
        <option value="sordariomycetes">sordariomycetes</option>
        <option value="saccharomycetes">saccharomycetes</option>
        <option value="saccharomycetales">saccharomycetales</option>
        <option value="basidiomycota">basidiomycota</option>
        <option value="microsporidia">microsporidia</option>
        <option value="embryophyta">embryophyta</option>
        <option value="protists">protists</option>
        <option value="alveolata_stramenophiles">alveolata_stramenophiles</option>
    </xml>
</macros>