Mercurial > repos > galaxyp > eggnog_mapper
diff eggnog_macros.xml @ 6:1d6c4af4b7bc draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
| author | galaxyp |
|---|---|
| date | Fri, 19 Feb 2021 18:53:12 +0000 |
| parents | 59501122d153 |
| children | 9d426cb7823b |
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--- a/eggnog_macros.xml Mon Nov 11 11:48:52 2019 -0500 +++ b/eggnog_macros.xml Fri Feb 19 18:53:12 2021 +0000 @@ -1,9 +1,18 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">1.0.3</token> + <token name="@VERSION@">2.0.1</token> + <token name="@EGGNOG_DB_VERSION@">2.0</token> + <!-- + # Versionning is super confusing: + # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) + # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) + # db v4.5 are not compatible with eggnog-mapper 2.0 + --> + <token name="@IDX_VERSION@">2.0</token> <xml name="citations"> <citations> <citation type="doi">10.1093/nar/gkv1248</citation> + <citation type="doi">10.1093/molbev/msx148</citation> </citations> </xml> <xml name="requirements"> @@ -16,119 +25,7 @@ </xml> <xml name="data_manager_params"> <param name="test" type="hidden" value="false" /> - <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/> - <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'"> - <option value="arch" selected="true">Archea arch_1 (arch)</option> - <option value="bact" selected="true">Bacteria bact_50 (bact)</option> - <option value="euk" selected="true">Eukaryote euk_500 (euk)</option> - <option value="NOG" selected="true">All organisms (NOG)</option> - <option value="aciNOG">Acidobacteria (aciNOG)</option> - <option value="acidNOG">Acidobacteriia (acidNOG)</option> - <option value="acoNOG">Aconoidasida (acoNOG)</option> - <option value="actNOG">Actinobacteria (actNOG)</option> - <option value="agaNOG">Agaricales (agaNOG)</option> - <option value="agarNOG">Agaricomycetes (agarNOG)</option> - <option value="apiNOG">Apicomplexa (apiNOG)</option> - <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option> - <option value="aquNOG">Aquificae (aquNOG)</option> - <option value="arNOG">Archaea (arNOG)</option> - <option value="arcNOG">Archaeoglobi (arcNOG)</option> - <option value="artNOG">Arthropoda (artNOG)</option> - <option value="arthNOG">Arthrodermataceae (arthNOG)</option> - <option value="ascNOG">Ascomycota (ascNOG)</option> - <option value="aveNOG">Aves (aveNOG)</option> - <option value="bacNOG">Bacilli (bacNOG)</option> - <option value="bactNOG">Bacteria (bactNOG)</option> - <option value="bacteNOG">Bacteroidia (bacteNOG)</option> - <option value="basNOG">Basidiomycota (basNOG)</option> - <option value="bctoNOG">Bacteroidetes (bctoNOG)</option> - <option value="biNOG">Bilateria (biNOG)</option> - <option value="bproNOG">Proteobacteria_beta (bproNOG)</option> - <option value="braNOG">Brassicales (braNOG)</option> - <option value="carNOG">Carnivora (carNOG)</option> - <option value="chaNOG">Chaetomiaceae (chaNOG)</option> - <option value="chlNOG">Chlorobi (chlNOG)</option> - <option value="chlaNOG">Chlamydiae (chlaNOG)</option> - <option value="chloNOG">Chloroflexi (chloNOG)</option> - <option value="chlorNOG">Chloroflexi (chlorNOG)</option> - <option value="chloroNOG">Chlorophyta (chloroNOG)</option> - <option value="chorNOG">Chordata (chorNOG)</option> - <option value="chrNOG">Chromadorea (chrNOG)</option> - <option value="cloNOG">Clostridia (cloNOG)</option> - <option value="cocNOG">Coccidia (cocNOG)</option> - <option value="creNOG">Crenarchaeota (creNOG)</option> - <option value="cryNOG">Cryptosporidiidae (cryNOG)</option> - <option value="cyaNOG">Cyanobacteria (cyaNOG)</option> - <option value="cytNOG">Cytophagia (cytNOG)</option> - <option value="debNOG">Debaryomycetaceae (debNOG)</option> - <option value="defNOG">Deferribacteres (defNOG)</option> - <option value="dehNOG">Dehalococcoidetes (dehNOG)</option> - <option value="deiNOG">Deinococcusthermus (deiNOG)</option> - <option value="delNOG">delta/epsilon (delNOG)</option> - <option value="dipNOG">Diptera (dipNOG)</option> - <option value="dotNOG">Dothideomycetes (dotNOG)</option> - <option value="dproNOG">Proteobacteria_delta (dproNOG)</option> - <option value="droNOG">Drosophilidae (droNOG)</option> - <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option> - <option value="eryNOG">Erysipelotrichi (eryNOG)</option> - <option value="euNOG">Eukaryotes (euNOG)</option> - <option value="eurNOG">Euryarchaeota (eurNOG)</option> - <option value="euroNOG">Eurotiomycetes (euroNOG)</option> - <option value="eurotNOG">Eurotiales (eurotNOG)</option> - <option value="fiNOG">Fishes (fiNOG)</option> - <option value="firmNOG">Firmicutes (firmNOG)</option> - <option value="flaNOG">Flavobacteriia (flaNOG)</option> - <option value="fuNOG">Fungi (fuNOG)</option> - <option value="fusoNOG">Fusobacteria (fusoNOG)</option> - <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option> - <option value="haeNOG">Haemosporida (haeNOG)</option> - <option value="halNOG">Halobacteria (halNOG)</option> - <option value="homNOG">Hominidae (homNOG)</option> - <option value="hymNOG">Hymenoptera (hymNOG)</option> - <option value="hypNOG">Hypocreales (hypNOG)</option> - <option value="inNOG">Insects (inNOG)</option> - <option value="kinNOG">Kinetoplastida (kinNOG)</option> - <option value="lepNOG">Lepidoptera (lepNOG)</option> - <option value="lilNOG">Liliopsida (lilNOG)</option> - <option value="maNOG">Mammals (maNOG)</option> - <option value="magNOG">Magnaporthales (magNOG)</option> - <option value="meNOG">Animals (meNOG)</option> - <option value="metNOG">Methanobacteria (metNOG)</option> - <option value="methNOG">Methanococci (methNOG)</option> - <option value="methaNOG">Methanomicrobia (methaNOG)</option> - <option value="necNOG">Nectriaceae (necNOG)</option> - <option value="negNOG">Negativicutes (negNOG)</option> - <option value="nemNOG">Nematodes (nemNOG)</option> - <option value="onyNOG">Onygenales (onyNOG)</option> - <option value="opiNOG">Opisthokonts (opiNOG)</option> - <option value="perNOG">Peronosporales (perNOG)</option> - <option value="plaNOG">Planctomycetes (plaNOG)</option> - <option value="pleNOG">Pleosporales (pleNOG)</option> - <option value="poaNOG">Poales (poaNOG)</option> - <option value="prNOG">Primates (prNOG)</option> - <option value="proNOG">Proteobacteria (proNOG)</option> - <option value="rhaNOG">Rhabditida (rhaNOG)</option> - <option value="roNOG">Rodents (roNOG)</option> - <option value="sacNOG">Saccharomycetaceae (sacNOG)</option> - <option value="saccNOG">Saccharomycetes (saccNOG)</option> - <option value="sorNOG">Sordariales (sorNOG)</option> - <option value="sordNOG">Sordariomycetes (sordNOG)</option> - <option value="sphNOG">Sphingobacteriia (sphNOG)</option> - <option value="spiNOG">Spirochaetes (spiNOG)</option> - <option value="spriNOG">Supraprimates (spriNOG)</option> - <option value="strNOG">Streptophyta (strNOG)</option> - <option value="synNOG">Synergistetes (synNOG)</option> - <option value="tenNOG">Tenericutes (tenNOG)</option> - <option value="thaNOG">Thaumarchaeota (thaNOG)</option> - <option value="theNOG">Thermoplasmata (theNOG)</option> - <option value="therNOG">Thermotogae (therNOG)</option> - <option value="thermNOG">Thermococci (thermNOG)</option> - <option value="treNOG">Tremellales (treNOG)</option> - <option value="veNOG">Vertebrates (veNOG)</option> - <option value="verNOG">Verrucomicrobia (verNOG)</option> - <option value="verrNOG">Verrucomicrobiae (verrNOG)</option> - <option value="virNOG">Viridiplantae (virNOG)</option> - </param> + <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/> </xml> <xml name="data_manager_outputs"> <outputs> @@ -141,33 +38,26 @@ #import os.path #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') #end if -#if $dbs: -#set $eggnogdbs = ' '.join(str($dbs).split(',')) -#else -#set $eggnogdbs = 'none' -#end if mkdir -p '${install_path}' && -download_eggnog_data.py - $diamond_database -y -q +download_eggnog_data.py + $diamond_database -y -q #if $test == 'true' -s #end if - --data_dir '$install_path' - $eggnogdbs && -python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs' + --data_dir '$install_path' && +python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' ]]></token> <xml name="data_manager_test"> - <!-- <test> <param name="test" value="true"/> - <param name="diamond_database" value="false"/> - <param name="dbs" value="thaNOG"/> + <param name="diamond_database" value="true"/> + <yield /> <output name="out_file"> <assert_contents> - <has_text text="eggnog_mapper_db" /> + <has_text text="eggnog_mapper_db_versioned" /> + <has_text text="@EGGNOG_DB_VERSION@" /> </assert_contents> </output> </test> - --> </xml> </macros>