Mercurial > repos > jjohnson > eggnog_mapper
view data_manager/data_manager_eggnog.xml @ 2:a74d61dbd155 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
author | jjohnson |
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date | Mon, 04 Nov 2019 16:38:44 -0500 |
parents | |
children | 9d94fe7ce8b9 |
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<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data"> <description>Download a new database</description> <macros> <token name="@VERSION@">4.5.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> </requirements> <version_command>emapper.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ #import json, os #set params = json.loads(open(str($out_file)).read()) #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') #if $dbs: #set $eggnogdbs = ' '.join($dbs.split(',')) #else #set $eggnogdbs = 'none' #endif #if $test == 'false' mkdir -p '${target_directory}' && download_eggnog_data.py $diamond_database -y -q --data_dir $install_path $eggnogdbs ' '.join(dbs.split(',')) && #end if python '${__tool_directory__}/data_manager_eggnog.py --config_file $out_file --install_path $target_directory --dbs '$dbs' ]]></command> <inputs> <param name="test" type="hidden" value="false" /> <param name="target_path" type="text" label="Download Destination (full path)" /> <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">eggnog_4.5.1 arch</option> <option value="bact" selected="true">eggnog_4.5.1 bact</option> <option value="euk" selected="true">eggnog_4.5.1 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> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> <tests> <test> <param name="test" value="true"/> <param name="diamond_database" value="false"/> <output name="out_file"> <assert_contents> <has_text text="eggnog_mapper_db" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ This tool downloads eggnog data using download_eggnog_data.py and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs. ]]></help> <citations> <citation type="doi">10.1093/nar/gkv1248</citation> </citations> </tool>