# HG changeset patch
# User galaxyp
# Date 1573491036 18000
# Node ID a5a3bdd0954bdc09dfeb768c25a862a59263a17e
# Parent  2667d24b58a0187d3c3c1ad6644396e3e47c4ed5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"

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
@@ -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 '$dbs'
+    ]]></token>
+    <xml name="data_manager_test">
+        <!--
+        <test>
+            <param name="test" value="true"/>
+            <param name="diamond_database" value="false"/>
+            <param name="dbs" value="thaNOG"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="eggnog_mapper_db" />
+                </assert_contents>
+            </output>
+        </test>
+        -->
+    </xml>
+</macros>
diff -r 2667d24b58a0 -r a5a3bdd0954b eggnog_mapper.xml
--- a/eggnog_mapper.xml	Wed Feb 28 13:20:40 2018 -0500
+++ b/eggnog_mapper.xml	Mon Nov 11 11:50:36 2019 -0500
@@ -1,19 +1,21 @@
-<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
+<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">
     <description>functional sequence annotation by orthology</description>
     <macros>
-        <token name="@VERSION@">1.0.3</token>
+        <import>eggnog_macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
-    </requirements>
-    <version_command>emapper.py --version</version_command>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
         emapper.py
-        --data_dir '$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">
+                            <!--
+                            <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>
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
@@ -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 - - -
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+//
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
@@ -0,0 +1,1465 @@
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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>
     <!-- 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>
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>
     <!-- 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>