Mercurial > repos > galaxyp > eggnog_mapper
changeset 5:a5a3bdd0954b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eggnog_macros.xml Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,173 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">1.0.3</token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/nar/gkv1248</citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>emapper.py --version</version_command> + </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> + </xml> + <xml name="data_manager_outputs"> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + </xml> + <token name="@DOWNLOAD_CMD@"><![CDATA[ +## tool should set install_path +#if $test == 'true' +#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 +#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 '$dbs' + ]]></token> + <xml name="data_manager_test"> + <!-- + <test> + <param name="test" value="true"/> + <param name="diamond_database" value="false"/> + <param name="dbs" value="thaNOG"/> + <output name="out_file"> + <assert_contents> + <has_text text="eggnog_mapper_db" /> + </assert_contents> + </output> + </test> + --> + </xml> +</macros>
--- a/eggnog_mapper.xml Wed Feb 28 13:20:40 2018 -0500 +++ b/eggnog_mapper.xml Mon Nov 11 11:50:36 2019 -0500 @@ -1,19 +1,21 @@ -<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@"> +<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1"> <description>functional sequence annotation by orthology</description> <macros> - <token name="@VERSION@">1.0.3</token> + <import>eggnog_macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> - </requirements> - <version_command>emapper.py --version</version_command> + <expand macro="requirements"/> + <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ emapper.py - --data_dir '$eggnog_data.fields.db' + --data_dir '$eggnog_data.fields.path' -m $db.mode $translate #if ($db.mode == 'hmmer'): - --database=$db.database.fields.db + #if $db.database.fields.path: + --database=$db.database.fields.path + #else + --database=$db.database + #end if #if $db.hmm_options.hmm_settings == 'specified': --hmm_maxhits=$db.hmm_options.hmm_maxhits --hmm_evalue=$db.hmm_options.hmm_evalue @@ -53,9 +55,7 @@ <inputs> <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> <param name="eggnog_data" type="select" label="Version of eggNOG Database"> - <options from_data_table="eggnog_mapper"> - <filter type="static_value" name="type" value="data" column="2"/> - </options> + <options from_data_table="eggnog_mapper_db"/> </param> <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" label="Are these coding DNA sequences that need to be translated?"/> @@ -66,9 +66,12 @@ </param> <when value="hmmer"> <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed."> - <options from_data_table="eggnog_mapper"> - <filter type="static_value" value="hmmer" column="2"/> + <options from_data_table="eggnog_mapper_hmm_dbs"> + <!-- + <filter type="param_value" ref="eggnog_data" column="1" /> + <filter type="unique_value" column="3" /> <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." /> + --> </options> </param> <conditional name="hmm_options"> @@ -395,15 +398,17 @@ <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> <param name="database" value="ENOG411CB2I"/> <param name="mode" value="hmmer"/> + <!-- <param name="test" value="true"/> - <param name="eggnog_data" value="eggNOG_4.5"/> + --> + <param name="eggnog_data" value="4.5"/> <param name="no_annot" value="true"/> <param name="no_file_comments" value="true"/> <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/> </test> <test> <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> - <param name="eggnog_data" value="eggNOG_4.5"/> <!-- not passed in test, but required for test to work --> + <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work --> <param name="no_annot" value="true"/> <param name="mode" value="diamond"/> <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> @@ -468,7 +473,5 @@ - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG ]]></help> - <citations> - <citation type="doi">10.1093/nar/gkv1248</citation> - </citations> + <expand macro="citations"/> </tool>
--- a/test-data/cached_locally/eggnog_mapper.loc Wed Feb 28 13:20:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#name value type db -eggnog_4.5 eggNOG_4.5 data ${__HERE__} -ENOG411CB2I ENOG411CB2I hmmer ${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I -dmnd diamond diamond ${__HERE__}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/eggnog_mapper_db.loc Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,2 @@ +#value name path +4.5 eggNOG_4.5 ${__HERE__}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,2 @@ +#key db_version value name path +4.5_ENOG411CB2I 4.5 ENOG411CB2I ENOG411CB2I ${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,637 @@ +HMMER3/f [3.1b1 | May 2013] +NAME thaNOG +LENG 205 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Thu Apr 16 06:29:18 2015 +NSEQ 3 +EFFN 0.454102 +CKSUM 2514733105 +STATS LOCAL MSV -10.6020 0.70508 +STATS LOCAL VITERBI -11.4006 0.70508 +STATS LOCAL FORWARD -4.9608 0.70508 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d + COMPO 2.60488 4.26537 2.86806 2.68812 3.48541 2.84597 3.68190 2.58658 2.57105 2.36046 3.71753 3.12796 3.51194 3.07828 3.00549 2.67857 2.91482 2.52396 5.16454 3.68907 + 2.68619 4.42226 2.77521 2.73125 3.46355 2.40514 3.72496 3.29355 2.67742 2.69356 4.24578 2.90348 2.73741 3.18148 2.89802 2.37888 2.77521 2.98520 4.58478 3.61505 + 0.17176 1.91497 4.55917 0.35031 1.21898 0.00000 * + 1 3.06761 4.52439 4.31327 3.78099 3.05250 4.16350 4.46561 2.17607 3.57234 1.30879 1.91901 4.09154 4.45690 3.86045 3.77957 3.51234 3.30962 2.23580 5.01687 3.83610 2 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 2 2.92273 5.02492 2.47434 1.07719 4.36685 3.25185 3.83632 3.81369 2.71243 3.43683 4.41304 2.91439 3.85493 3.05312 3.11711 2.90913 3.22689 3.50145 5.54519 4.26810 3 e - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 3 2.78351 4.58087 3.32911 2.88754 3.40933 3.59103 3.84122 2.81006 2.61259 1.66760 3.45029 3.30455 4.01739 2.39416 2.89621 2.95209 3.03282 2.70991 4.99124 3.67436 4 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 4 2.53418 4.23705 3.59368 3.16853 3.49025 3.42404 4.06074 1.74993 3.06664 2.43412 3.49971 3.45907 3.96332 3.42386 3.35145 2.21772 2.86823 2.25074 5.06222 3.78462 5 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 5 2.78589 5.09914 2.65704 2.00312 4.42838 3.36184 3.58271 3.84850 1.89046 3.35615 4.18804 2.85104 3.82604 2.22691 2.52714 2.75121 3.01078 3.49213 5.49453 4.17260 6 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 6 2.93327 5.02405 3.29627 2.69847 4.43219 3.55593 3.56756 3.79912 1.41937 3.28272 4.16078 3.11215 3.94769 2.71245 1.76026 2.94298 3.11879 3.48852 5.35872 4.16856 7 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 7 2.42315 4.21787 3.44026 2.97006 3.62502 3.28653 3.93296 2.25259 2.89478 2.62127 3.57447 3.29089 3.83488 3.23909 3.22031 2.19519 2.23227 2.47087 5.09408 3.85175 8 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 8 3.00341 4.43279 4.28393 3.89883 3.35077 4.02713 4.63395 1.12320 3.72623 1.94475 3.29234 4.14920 4.46227 4.07854 3.92692 3.51945 3.30343 1.84653 5.23382 3.96866 9 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 9 3.11581 4.58898 4.13200 3.77226 3.12310 3.93638 4.43920 2.32589 3.54034 0.92039 3.15824 4.05113 4.37826 3.91722 3.72201 3.50392 3.41191 2.35386 4.98887 3.70377 10 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 10 2.21970 4.14708 3.27216 2.97236 4.05658 2.94753 4.04583 3.36566 2.97325 3.13664 4.01775 3.19548 3.65760 3.31810 3.28297 1.86435 1.69294 2.93575 5.43271 4.18954 11 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.idmap Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,1465 @@ + +1 thaNOG.ENOG411CBXW.meta_raw +2 thaNOG.ENOG411CB9A.meta_raw +3 thaNOG.ENOG411CBE9.meta_raw +4 thaNOG.ENOG411CBDJ.meta_raw +5 thaNOG.ENOG411CC6Z.meta_raw +6 thaNOG.ENOG411CBDE.meta_raw +7 thaNOG.ENOG411CC3U.meta_raw +8 thaNOG.ENOG411CBAN.meta_raw +9 thaNOG.ENOG411CBN8.meta_raw +10 thaNOG.ENOG411CC99.meta_raw +11 thaNOG.ENOG411CC08.meta_raw +12 thaNOG.ENOG411CBZ3.meta_raw +13 thaNOG.ENOG411CBTB.meta_raw +14 thaNOG.ENOG411CB5Y.meta_raw +15 thaNOG.ENOG411CBTK.meta_raw +16 thaNOG.ENOG411CCB4.meta_raw +17 thaNOG.ENOG411CBCR.meta_raw +18 thaNOG.ENOG411CC69.meta_raw +19 thaNOG.ENOG411CB7A.meta_raw +20 thaNOG.ENOG411CBNA.meta_raw +21 thaNOG.ENOG411CBB9.meta_raw +22 thaNOG.ENOG411CBWE.meta_raw +23 thaNOG.ENOG411CCBA.meta_raw +24 thaNOG.ENOG411CC4D.meta_raw +25 thaNOG.ENOG411CC9I.meta_raw +26 thaNOG.ENOG411CBCM.meta_raw 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--- a/tool-data/eggnog_mapper.loc.sample Wed Feb 28 13:20:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of eggnog_mapper data files. -# -# eggnog-mapper requires the following files to be installed in the data directory: -# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz -# In addition individual HMM DBs can be installed from: -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ -# A complete diamond database is available from: -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz -# -# The python script download_eggnog_data.py, -# included with eggnog_mapper, can be used to download the files to the correct directory -# -# The near-equivalence of columns "value" and "db" is needed for the tests to work, -# and for the setting of --data_dir to the parent directory of eggnog.db -# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. -# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases -# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, -# value and db should be the same (in the example, both should be "thaNOG") -# -# -#name value type db -#eggnog_4.5 eggnog_4.5 data /path/to/directory/that/contains/eggnog.db -#Full eggNOG database NOG hmmer NOG -#Eukaryotes euk hmmer euk -#Bacteria bact hmmer bact -#Archaea arch hmmer arch -#dmnd diamond diamond dmnd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_db.loc.sample Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,25 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz +# In addition individual HMM DBs can be installed from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ +# A complete diamond database is available from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#db_version name path +#4.5.1 eggnog_4.5.1 /path/to/directory/that/contains/eggnog.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_hmm_dbs.loc.sample Mon Nov 11 11:50:36 2019 -0500 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz +# In addition individual HMM DBs can be installed from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ +# A complete diamond database is available from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#key db_version value name path +#4.5.1_NOG 4.5.1 NOG Full eggNOG database (NOG) +#4.5.1_euk 4.5.1 euk Eukaryotes (euk) +#4.5.1_aproNOG 4.5.1 aproNOG Proteobacteria_alpha (aproNOG) +#4.5.1_aproNOG 4.5.1 ENOG411CB2I ENOG411CB2I (custom) /path/to/custom/hmmdb/ENOG411CB2I
--- a/tool_data_table_conf.xml.sample Wed Feb 28 13:20:40 2018 -0500 +++ b/tool_data_table_conf.xml.sample Mon Nov 11 11:50:36 2019 -0500 @@ -1,7 +1,11 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper" comment_char="#"> - <columns>name,value,type,db</columns> - <file path="tool-data/eggnog_mapper.loc" /> + <table name="eggnog_mapper_db" comment_char="#" allow_duplicate_entries="False"> + <columns>value,name,path</columns> + <file path="tool-data/eggnog_mapper_db.loc" /> + </table> + <table name="eggnog_mapper_hmm_dbs" comment_char="#" allow_duplicate_entries="False"> + <columns>key,db_version,value,name,path</columns> + <file path="tool-data/eggnog_mapper_hmm_dbs.loc" /> </table> </tables>
--- a/tool_data_table_conf.xml.test Wed Feb 28 13:20:40 2018 -0500 +++ b/tool_data_table_conf.xml.test Mon Nov 11 11:50:36 2019 -0500 @@ -1,7 +1,11 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper" comment_char="#"> - <columns>name,value,type,db</columns> - <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper.loc" /> + <table name="eggnog_mapper_db" comment_char="#"> + <columns>value,name,path</columns> + <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" /> + </table> + <table name="eggnog_mapper_hmm_dbs" comment_char="#"> + <columns>key,db_version,value,name,path</columns> + <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc" /> </table> </tables>