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Changeset 5:a5a3bdd0954b (2019-11-11)

Previous changeset 4:2667d24b58a0 (2018-02-28) Next changeset 6:3cb37af59360 (2020-09-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"

modified:
eggnog_mapper.xml
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

removed:
test-data/cached_locally/eggnog_mapper.loc
tool-data/eggnog_mapper.loc.sample

diff -r 2667d24b58a0 -r a5a3bdd0954b eggnog_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eggnog_macros.xml Mon Nov 11 11:50:36 2019 -0500

[

b'@@ -0,0 +1,173 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@VERSION@">1.0.3</token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkv1248</citation>\n+ </citations>\n+ </xml>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command>emapper.py --version</version_command>\n+ </xml>\n+ <xml name="data_manager_params">\n+ <param name="test" type="hidden" value="false" />\n+ <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>\n+ <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used\'">\n+ <option value="arch" selected="true">Archea arch_1 (arch)</option>\n+ <option value="bact" selected="true">Bacteria bact_50 (bact)</option>\n+ <option value="euk" selected="true">Eukaryote euk_500 (euk)</option>\n+ <option value="NOG" selected="true">All organisms (NOG)</option>\n+ <option value="aciNOG">Acidobacteria (aciNOG)</option>\n+ <option value="acidNOG">Acidobacteriia (acidNOG)</option>\n+ <option value="acoNOG">Aconoidasida (acoNOG)</option>\n+ <option value="actNOG">Actinobacteria (actNOG)</option>\n+ <option value="agaNOG">Agaricales (agaNOG)</option>\n+ <option value="agarNOG">Agaricomycetes (agarNOG)</option>\n+ <option value="apiNOG">Apicomplexa (apiNOG)</option>\n+ <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>\n+ <option value="aquNOG">Aquificae (aquNOG)</option>\n+ <option value="arNOG">Archaea (arNOG)</option>\n+ <option value="arcNOG">Archaeoglobi (arcNOG)</option>\n+ <option value="artNOG">Arthropoda (artNOG)</option>\n+ <option value="arthNOG">Arthrodermataceae (arthNOG)</option>\n+ <option value="ascNOG">Ascomycota (ascNOG)</option>\n+ <option value="aveNOG">Aves (aveNOG)</option>\n+ <option value="bacNOG">Bacilli (bacNOG)</option>\n+ <option value="bactNOG">Bacteria (bactNOG)</option>\n+ <option value="bacteNOG">Bacteroidia (bacteNOG)</option>\n+ <option value="basNOG">Basidiomycota (basNOG)</option>\n+ <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>\n+ <option value="biNOG">Bilateria (biNOG)</option>\n+ <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>\n+ <option value="braNOG">Brassicales (braNOG)</option>\n+ <option value="carNOG">Carnivora (carNOG)</option>\n+ <option value="chaNOG">Chaetomiaceae (chaNOG)</option>\n+ <option value="chlNOG">Chlorobi (chlNOG)</option>\n+ <option value="chlaNOG">Chlamydiae (chlaNOG)</option>\n+ <option value="chloNOG">Chloroflexi (chloNOG)</option>\n+ <option value="chlorNOG">Chloroflexi (chlorNOG)</option>\n+ <option value="chloroNOG">Chlorophyta (chloroNOG)</option>\n+ <option value="chorNOG">Chordata (chorNOG)</option>\n+ <option value="chrNOG">Chromadorea (chrNOG)</option>\n+ <option value="cloNOG">Clostridia (cloNOG)</option>\n+ <option value="cocNOG">Coccidia (cocNOG)</option>\n+ <option value="creNOG">Crenarchaeota (creNOG)</option>\n+ <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>\n+ <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>\n+ <option value="cytNOG">Cytophagia (cytNOG)</option>\n+ <option value="debNOG">Debaryomycetaceae (debNOG)</option>\n+ <option value="defNOG">Deferribacteres (defNOG)</option>\n+ <option value="dehNOG">Dehalococcoidetes (dehNOG)</'..b' <option value="lepNOG">Lepidoptera (lepNOG)</option>\n+ <option value="lilNOG">Liliopsida (lilNOG)</option>\n+ <option value="maNOG">Mammals (maNOG)</option>\n+ <option value="magNOG">Magnaporthales (magNOG)</option>\n+ <option value="meNOG">Animals (meNOG)</option>\n+ <option value="metNOG">Methanobacteria (metNOG)</option>\n+ <option value="methNOG">Methanococci (methNOG)</option>\n+ <option value="methaNOG">Methanomicrobia (methaNOG)</option>\n+ <option value="necNOG">Nectriaceae (necNOG)</option>\n+ <option value="negNOG">Negativicutes (negNOG)</option>\n+ <option value="nemNOG">Nematodes (nemNOG)</option>\n+ <option value="onyNOG">Onygenales (onyNOG)</option>\n+ <option value="opiNOG">Opisthokonts (opiNOG)</option>\n+ <option value="perNOG">Peronosporales (perNOG)</option>\n+ <option value="plaNOG">Planctomycetes (plaNOG)</option>\n+ <option value="pleNOG">Pleosporales (pleNOG)</option>\n+ <option value="poaNOG">Poales (poaNOG)</option>\n+ <option value="prNOG">Primates (prNOG)</option>\n+ <option value="proNOG">Proteobacteria (proNOG)</option>\n+ <option value="rhaNOG">Rhabditida (rhaNOG)</option>\n+ <option value="roNOG">Rodents (roNOG)</option>\n+ <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>\n+ <option value="saccNOG">Saccharomycetes (saccNOG)</option>\n+ <option value="sorNOG">Sordariales (sorNOG)</option>\n+ <option value="sordNOG">Sordariomycetes (sordNOG)</option>\n+ <option value="sphNOG">Sphingobacteriia (sphNOG)</option>\n+ <option value="spiNOG">Spirochaetes (spiNOG)</option>\n+ <option value="spriNOG">Supraprimates (spriNOG)</option>\n+ <option value="strNOG">Streptophyta (strNOG)</option>\n+ <option value="synNOG">Synergistetes (synNOG)</option>\n+ <option value="tenNOG">Tenericutes (tenNOG)</option>\n+ <option value="thaNOG">Thaumarchaeota (thaNOG)</option>\n+ <option value="theNOG">Thermoplasmata (theNOG)</option>\n+ <option value="therNOG">Thermotogae (therNOG)</option>\n+ <option value="thermNOG">Thermococci (thermNOG)</option>\n+ <option value="treNOG">Tremellales (treNOG)</option>\n+ <option value="veNOG">Vertebrates (veNOG)</option>\n+ <option value="verNOG">Verrucomicrobia (verNOG)</option>\n+ <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>\n+ <option value="virNOG">Viridiplantae (virNOG)</option>\n+ </param>\n+ </xml>\n+ <xml name="data_manager_outputs">\n+ <outputs>\n+ <data name="out_file" format="data_manager_json" label="${tool.name}"/>\n+ </outputs>\n+ </xml>\n+ <token name="@DOWNLOAD_CMD@"><![CDATA[\n+## tool should set install_path\n+#if $test == \'true\'\n+#import os.path\n+#set $install_path = $os.path.join($os.path.dirname($__tool_directory__), \'test-data/cached_locally\')\n+#end if\n+#if $dbs:\n+#set $eggnogdbs = \' \'.join(str($dbs).split(\',\'))\n+#else\n+#set $eggnogdbs = \'none\'\n+#end if\n+mkdir -p \'${install_path}\' &&\n+download_eggnog_data.py \n+ $diamond_database -y -q \n+#if $test == \'true\'\n+ -s\n+#end if\n+ --data_dir \'$install_path\' \n+ $eggnogdbs &&\n+python \'${__tool_directory__}/data_manager_eggnog.py\' --config_file \'$out_file\' --install_path \'$install_path\' --dbs \'$dbs\'\n+ ]]></token>\n+ <xml name="data_manager_test">\n+ \n+ </xml>\n+</macros>\n'

diff -r 2667d24b58a0 -r a5a3bdd0954b eggnog_mapper.xml
--- 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">
+                            
                         </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="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"/> 
+            <param name="eggnog_data" value="4.5"/> 
             <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>

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/eggnog_mapper.loc
--- 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__}

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/eggnog_mapper_db.loc
--- /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__}

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/eggnog_mapper_hmm_dbs.loc
--- /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

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG
--- /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

[

b'@@ -0,0 +1,637 @@\n+HMMER3/f [3.1b1 | May 2013]\n+NAME thaNOG\n+LENG 205\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Apr 16 06:29:18 2015\n+NSEQ 3\n+EFFN 0.454102\n+CKSUM 2514733105\n+STATS LOCAL MSV -10.6020 0.70508\n+STATS LOCAL VITERBI -11.4006 0.70508\n+STATS LOCAL FORWARD -4.9608 0.70508\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ 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\n+ 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\n+ 0.17176 1.91497 4.55917 0.35031 1.21898 0.00000 *\n+ 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 - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 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 - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 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 - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 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 - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 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 - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 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 - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 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'..b'.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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 198 3.19664 4.70006 3.78606 3.50925 2.29569 3.78896 3.60349 3.21093 3.36780 2.67393 3.88982 3.68029 4.26389 3.68239 3.55861 3.33670 3.48329 3.07987 3.93791 1.02720 199 y - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 199 2.62209 4.40041 3.28850 3.18371 4.32546 0.78630 4.30564 3.91689 3.36007 3.57539 4.55128 3.45295 3.79040 3.68714 3.59951 2.79308 3.10058 3.45214 5.42949 4.42634 200 g - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 200 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 201 e - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 201 2.29842 4.21804 3.17637 2.99106 4.04109 2.94862 4.10162 3.55914 3.06240 3.28234 4.21181 3.22118 3.68461 3.41464 3.34915 1.14610 2.77598 3.10206 5.41656 4.12456 202 s - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 202 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 203 i - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 203 2.95756 4.78041 3.09252 2.84941 3.26099 3.41845 1.21998 3.65490 2.69349 3.15313 4.19373 3.25996 3.96930 3.21533 2.96107 3.02872 3.25993 3.39076 4.72643 3.21297 204 h - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 204 2.62209 4.40041 3.28850 3.18371 4.32546 0.78630 4.30564 3.91689 3.36007 3.57539 4.55128 3.45295 3.79040 3.68714 3.59951 2.79308 3.10058 3.45214 5.42949 4.42634 205 g - - -\n+ 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\n+ 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n+ 205 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 206 i - - -\n+ 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\n+ 0.02203 3.82629 * 0.61958 0.77255 0.00000 *\n+//\n'

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3f

Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3f has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3i

Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3i has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3m

Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3m has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3p

Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3p has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3f

Binary file test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3f has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3i

Binary file test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3i has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3m

Binary file test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3m has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3p

Binary file test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3p has changed

diff -r 2667d24b58a0 -r a5a3bdd0954b test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.idmap
--- /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

b'@@ -0,0 +1,1465 @@\n+ \n+1 thaNOG.ENOG411CBXW.meta_raw\n+2 thaNOG.ENOG411CB9A.meta_raw\n+3 thaNOG.ENOG411CBE9.meta_raw\n+4 thaNOG.ENOG411CBDJ.meta_raw\n+5 thaNOG.ENOG411CC6Z.meta_raw\n+6 thaNOG.ENOG411CBDE.meta_raw\n+7 thaNOG.ENOG411CC3U.meta_raw\n+8 thaNOG.ENOG411CBAN.meta_raw\n+9 thaNOG.ENOG411CBN8.meta_raw\n+10 thaNOG.ENOG411CC99.meta_raw\n+11 thaNOG.ENOG411CC08.meta_raw\n+12 thaNOG.ENOG411CBZ3.meta_raw\n+13 thaNOG.ENOG411CBTB.meta_raw\n+14 thaNOG.ENOG411CB5Y.meta_raw\n+15 thaNOG.ENOG411CBTK.meta_raw\n+16 thaNOG.ENOG411CCB4.meta_raw\n+17 thaNOG.ENOG411CBCR.meta_raw\n+18 thaNOG.ENOG411CC69.meta_raw\n+19 thaNOG.ENOG411CB7A.meta_raw\n+20 thaNOG.ENOG411CBNA.meta_raw\n+21 thaNOG.ENOG411CBB9.meta_raw\n+22 thaNOG.ENOG411CBWE.meta_raw\n+23 thaNOG.ENOG411CCBA.meta_raw\n+24 thaNOG.ENOG411CC4D.meta_raw\n+25 thaNOG.ENOG411CC9I.meta_raw\n+26 thaNOG.ENOG411CBCM.meta_raw\n+27 thaNOG.ENOG411CBZ6.meta_raw\n+28 thaNOG.ENOG411CBZV.meta_raw\n+29 thaNOG.ENOG411CBBR.meta_raw\n+30 thaNOG.ENOG411CBGU.meta_raw\n+31 thaNOG.ENOG411CBBB.meta_raw\n+32 thaNOG.ENOG411CBEW.meta_raw\n+33 thaNOG.ENOG411CC6X.meta_raw\n+34 thaNOG.ENOG411CC8E.meta_raw\n+35 thaNOG.ENOG411CBXR.meta_raw\n+36 thaNOG.ENOG411CC5U.meta_raw\n+37 thaNOG.ENOG411CBAJ.meta_raw\n+38 thaNOG.ENOG411CBDV.meta_raw\n+39 thaNOG.ENOG411CBRB.meta_raw\n+40 thaNOG.ENOG411CB60.meta_raw\n+41 thaNOG.ENOG411CBNP.meta_raw\n+42 thaNOG.ENOG411CB8J.meta_raw\n+43 thaNOG.ENOG411CBT9.meta_raw\n+44 thaNOG.ENOG411CBJ5.meta_raw\n+45 thaNOG.ENOG411CB5T.meta_raw\n+46 thaNOG.ENOG411CBN2.meta_raw\n+47 thaNOG.ENOG411CBMW.meta_raw\n+48 thaNOG.ENOG411CBGJ.meta_raw\n+49 thaNOG.ENOG411CB56.meta_raw\n+50 thaNOG.ENOG411CB47.meta_raw\n+51 thaNOG.ENOG411CBI7.meta_raw\n+52 thaNOG.ENOG411CBY7.meta_raw\n+53 thaNOG.ENOG411CBIS.meta_raw\n+54 thaNOG.ENOG411CBP3.meta_raw\n+55 thaNOG.ENOG411CBXK.meta_raw\n+56 thaNOG.ENOG411CBT6.meta_raw\n+57 thaNOG.ENOG411CBCT.meta_raw\n+58 thaNOG.ENOG411CBJT.meta_raw\n+59 thaNOG.ENOG411CBJ9.meta_raw\n+60 thaNOG.ENOG411CBN3.meta_raw\n+61 thaNOG.ENOG411CBR1.meta_raw\n+62 thaNOG.ENOG411CBKA.meta_raw\n+63 thaNOG.ENOG411CBY9.meta_raw\n+64 thaNOG.ENOG411CBNK.meta_raw\n+65 thaNOG.ENOG411CC8I.meta_raw\n+66 thaNOG.ENOG411CBN0.meta_raw\n+67 thaNOG.ENOG411CBP2.meta_raw\n+68 thaNOG.ENOG411CBDZ.meta_raw\n+69 thaNOG.ENOG411CC0R.meta_raw\n+70 thaNOG.ENOG411CBRC.meta_raw\n+71 thaNOG.ENOG411CBF2.meta_raw\n+72 thaNOG.ENOG411CC3S.meta_raw\n+73 thaNOG.ENOG411CBIX.meta_raw\n+74 thaNOG.ENOG411CBMB.meta_raw\n+75 thaNOG.ENOG411CB4H.meta_raw\n+76 thaNOG.ENOG411CB4G.meta_raw\n+77 thaNOG.ENOG411CBC0.meta_raw\n+78 thaNOG.ENOG411CBFX.meta_raw\n+79 thaNOG.ENOG411CC30.meta_raw\n+80 thaNOG.ENOG411CBSC.meta_raw\n+81 thaNOG.ENOG411CBRN.meta_raw\n+82 thaNOG.ENOG411CBAA.meta_raw\n+83 thaNOG.ENOG411CBPY.meta_raw\n+84 thaNOG.ENOG411CBDW.meta_raw\n+85 thaNOG.ENOG411CBMS.meta_raw\n+86 thaNOG.ENOG411CBP1.meta_raw\n+87 thaNOG.ENOG411CBB3.meta_raw\n+88 thaNOG.ENOG411CB74.meta_raw\n+89 thaNOG.ENOG411CC4M.meta_raw\n+90 thaNOG.ENOG411CC9S.meta_raw\n+91 thaNOG.ENOG411CBZE.meta_raw\n+92 thaNOG.ENOG411CC6C.meta_raw\n+93 thaNOG.ENOG411CBID.meta_raw\n+94 thaNOG.ENOG411CBXY.meta_raw\n+95 thaNOG.ENOG411CB4A.meta_raw\n+96 thaNOG.ENOG411CBGZ.meta_raw\n+97 thaNOG.ENOG411CBU5.meta_raw\n+98 thaNOG.ENOG411CBJC.meta_raw\n+99 thaNOG.ENOG411CB34.meta_raw\n+100 thaNOG.ENOG411CBXH.meta_raw\n+101 thaNOG.ENOG411CB44.meta_raw\n+102 thaNOG.ENOG411CBAI.meta_raw\n+103 thaNOG.ENOG411CC4Y.meta_raw\n+104 thaNOG.ENOG411CBQV.meta_raw\n+105 thaNOG.ENOG411CC26.meta_raw\n+106 thaNOG.ENOG411CBC2.meta_raw\n+107 thaNOG.ENOG411CB8B.meta_raw\n+108 thaNOG.ENOG411CBH2.meta_raw\n+109 thaNOG.ENOG411CBCU.meta_raw\n+110 thaNOG.ENOG411CBG2.meta_raw\n+111 thaNOG.ENOG411CBDX.meta_raw\n+112 thaNOG.ENOG411CBW6.meta_raw\n+113 thaNOG.ENOG411CB84.meta_raw\n+114 thaNOG.ENOG411CB97.meta_raw\n+115 thaNOG.ENOG411CBUX.meta_raw\n+116 thaNOG.ENOG411CBJH.meta_raw\n+117 thaNOG.ENOG411CBCC.meta_raw\n+118 thaNOG.ENOG411CC7R.meta_raw\n+119 thaNOG.ENOG411CBNW.meta_raw\n+120 thaNOG.ENOG411CB9H.meta_raw\n+121 thaNOG.ENOG411CBRZ.meta_raw\n+122 thaNOG.ENOG411CB4W.meta_raw\n+123 thaNOG.ENOG411CBBI.meta_raw\n+124 thaNOG.ENOG411CB6U.me'..b'ENOG411CBFB.meta_raw\n+1348 thaNOG.ENOG411CB7V.meta_raw\n+1349 thaNOG.ENOG411CB68.meta_raw\n+1350 thaNOG.ENOG411CBQH.meta_raw\n+1351 thaNOG.ENOG411CBWG.meta_raw\n+1352 thaNOG.ENOG411CC01.meta_raw\n+1353 thaNOG.ENOG411CBNU.meta_raw\n+1354 thaNOG.ENOG411CB4E.meta_raw\n+1355 thaNOG.ENOG411CBYC.meta_raw\n+1356 thaNOG.ENOG411CBA9.meta_raw\n+1357 thaNOG.ENOG411CB82.meta_raw\n+1358 thaNOG.ENOG411CCAM.meta_raw\n+1359 thaNOG.ENOG411CBSE.meta_raw\n+1360 thaNOG.ENOG411CBTG.meta_raw\n+1361 thaNOG.ENOG411CBIZ.meta_raw\n+1362 thaNOG.ENOG411CBNB.meta_raw\n+1363 thaNOG.ENOG411CBJ7.meta_raw\n+1364 thaNOG.ENOG411CBYW.meta_raw\n+1365 thaNOG.ENOG411CC0M.meta_raw\n+1366 thaNOG.ENOG411CBNX.meta_raw\n+1367 thaNOG.ENOG411CB6K.meta_raw\n+1368 thaNOG.ENOG411CBD3.meta_raw\n+1369 thaNOG.ENOG411CC4F.meta_raw\n+1370 thaNOG.ENOG411CC43.meta_raw\n+1371 thaNOG.ENOG411CC8Q.meta_raw\n+1372 thaNOG.ENOG411CBUT.meta_raw\n+1373 thaNOG.ENOG411CBM7.meta_raw\n+1374 thaNOG.ENOG411CBH4.meta_raw\n+1375 thaNOG.ENOG411CC5M.meta_raw\n+1376 thaNOG.ENOG411CBTT.meta_raw\n+1377 thaNOG.ENOG411CB5U.meta_raw\n+1378 thaNOG.ENOG411CC9D.meta_raw\n+1379 thaNOG.ENOG411CBX8.meta_raw\n+1380 thaNOG.ENOG411CBGT.meta_raw\n+1381 thaNOG.ENOG411CBQD.meta_raw\n+1382 thaNOG.ENOG411CBX6.meta_raw\n+1383 thaNOG.ENOG411CBGV.meta_raw\n+1384 thaNOG.ENOG411CC97.meta_raw\n+1385 thaNOG.ENOG411CBMT.meta_raw\n+1386 thaNOG.ENOG411CBFS.meta_raw\n+1387 thaNOG.ENOG411CBS7.meta_raw\n+1388 thaNOG.ENOG411CBHF.meta_raw\n+1389 thaNOG.ENOG411CBS2.meta_raw\n+1390 thaNOG.ENOG411CBNR.meta_raw\n+1391 thaNOG.ENOG411CC5R.meta_raw\n+1392 thaNOG.ENOG411CBAE.meta_raw\n+1393 thaNOG.ENOG411CBWX.meta_raw\n+1394 thaNOG.ENOG411CC7U.meta_raw\n+1395 thaNOG.ENOG411CC3R.meta_raw\n+1396 thaNOG.ENOG411CC8P.meta_raw\n+1397 thaNOG.ENOG411CC3F.meta_raw\n+1398 thaNOG.ENOG411CBBZ.meta_raw\n+1399 thaNOG.ENOG411CBM5.meta_raw\n+1400 thaNOG.ENOG411CB4R.meta_raw\n+1401 thaNOG.ENOG411CBH9.meta_raw\n+1402 thaNOG.ENOG411CBU4.meta_raw\n+1403 thaNOG.ENOG411CBQ4.meta_raw\n+1404 thaNOG.ENOG411CB37.meta_raw\n+1405 thaNOG.ENOG411CC1T.meta_raw\n+1406 thaNOG.ENOG411CC96.meta_raw\n+1407 thaNOG.ENOG411CB8X.meta_raw\n+1408 thaNOG.ENOG411CBRX.meta_raw\n+1409 thaNOG.ENOG411CBC5.meta_raw\n+1410 thaNOG.ENOG411CBQ7.meta_raw\n+1411 thaNOG.ENOG411CBVK.meta_raw\n+1412 thaNOG.ENOG411CBQJ.meta_raw\n+1413 thaNOG.ENOG411CBSI.meta_raw\n+1414 thaNOG.ENOG411CBD1.meta_raw\n+1415 thaNOG.ENOG411CC24.meta_raw\n+1416 thaNOG.ENOG411CCA4.meta_raw\n+1417 thaNOG.ENOG411CC72.meta_raw\n+1418 thaNOG.ENOG411CBQ2.meta_raw\n+1419 thaNOG.ENOG411CB5Q.meta_raw\n+1420 thaNOG.ENOG411CBA0.meta_raw\n+1421 thaNOG.ENOG411CC6G.meta_raw\n+1422 thaNOG.ENOG411CBQ1.meta_raw\n+1423 thaNOG.ENOG411CCAE.meta_raw\n+1424 thaNOG.ENOG411CCA3.meta_raw\n+1425 thaNOG.ENOG411CBNM.meta_raw\n+1426 thaNOG.ENOG411CBZ5.meta_raw\n+1427 thaNOG.ENOG411CC9J.meta_raw\n+1428 thaNOG.ENOG411CBRH.meta_raw\n+1429 thaNOG.ENOG411CBFC.meta_raw\n+1430 thaNOG.ENOG411CBJV.meta_raw\n+1431 thaNOG.ENOG411CBJS.meta_raw\n+1432 thaNOG.ENOG411CBZW.meta_raw\n+1433 thaNOG.ENOG411CBQQ.meta_raw\n+1434 thaNOG.ENOG411CBQA.meta_raw\n+1435 thaNOG.ENOG411CBG7.meta_raw\n+1436 thaNOG.ENOG411CBGD.meta_raw\n+1437 thaNOG.ENOG411CB9Y.meta_raw\n+1438 thaNOG.ENOG411CB2R.meta_raw\n+1439 thaNOG.ENOG411CB9U.meta_raw\n+1440 thaNOG.ENOG411CBWS.meta_raw\n+1441 thaNOG.ENOG411CBWQ.meta_raw\n+1442 thaNOG.ENOG411CB7Q.meta_raw\n+1443 thaNOG.ENOG411CBMM.meta_raw\n+1444 thaNOG.ENOG411CBRG.meta_raw\n+1445 thaNOG.ENOG411CBG1.meta_raw\n+1446 thaNOG.ENOG411CC8W.meta_raw\n+1447 thaNOG.ENOG411CBBG.meta_raw\n+1448 thaNOG.ENOG411CB8S.meta_raw\n+1449 thaNOG.ENOG411CC5F.meta_raw\n+1450 thaNOG.ENOG411CBC9.meta_raw\n+1451 thaNOG.ENOG411CBHE.meta_raw\n+1452 thaNOG.ENOG411CBPR.meta_raw\n+1453 thaNOG.ENOG411CB88.meta_raw\n+1454 thaNOG.ENOG411CBV1.meta_raw\n+1455 thaNOG.ENOG411CC9N.meta_raw\n+1456 thaNOG.ENOG411CBK9.meta_raw\n+1457 thaNOG.ENOG411CB8F.meta_raw\n+1458 thaNOG.ENOG411CBVZ.meta_raw\n+1459 thaNOG.ENOG411CC5S.meta_raw\n+1460 thaNOG.ENOG411CBXJ.meta_raw\n+1461 thaNOG.ENOG411CC0E.meta_raw\n+1462 thaNOG.ENOG411CBHU.meta_raw\n+1463 thaNOG.ENOG411CBHT.meta_raw\n+1464 thaNOG.ENOG411CB87.meta_raw\n'

diff -r 2667d24b58a0 -r a5a3bdd0954b tool-data/eggnog_mapper.loc.sample
--- 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

diff -r 2667d24b58a0 -r a5a3bdd0954b tool-data/eggnog_mapper_db.loc.sample
--- /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

diff -r 2667d24b58a0 -r a5a3bdd0954b tool-data/eggnog_mapper_hmm_dbs.loc.sample
--- /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

diff -r 2667d24b58a0 -r a5a3bdd0954b tool_data_table_conf.xml.sample
--- 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>
     
-    <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>

diff -r 2667d24b58a0 -r a5a3bdd0954b tool_data_table_conf.xml.test
--- 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>
     
-    <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>