# HG changeset patch
# User galaxyp
# Date 1509473870 14400
# Node ID f4e5279b5d1054401c59bd88a502a9751c4b05ac

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

diff -r 000000000000 -r f4e5279b5d10 eggnog_mapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eggnog_mapper.xml	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,470 @@
+<tool id="eggnog_mapper" name="eggNOG Mapper" version="1.0.1">
+    <description>functional sequence annotation by orthology</description>
+    <requirements>
+        <requirement type="package" version="1.0.1">eggnog-mapper</requirement>
+    </requirements>
+    <version_command>emapper.py --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        emapper.py
+        --data_dir '$eggnog_data.fields.db'
+        -m $db.mode 
+        $translate
+        #if ($db.mode == 'hmmer'):
+            --database=$db.database.fields.db
+            #if $db.hmm_options.hmm_settings == 'specified':
+                --hmm_maxhits=$db.hmm_options.hmm_maxhits
+                --hmm_evalue=$db.hmm_options.hmm_evalue
+                --hmm_score=$db.hmm_options.hmm_score
+                --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
+                #if str($db.hmm_options.hmm_qcov):
+                    --hmm_qcov=$db.hmm_options.hmm_qcov
+                #end if
+                --Z=$db.hmm_options.Z
+            #end if
+        #elif ($db.mode == 'diamond'):
+            --matrix '$db.matrix_gapcosts.matrix'
+            $db.matrix_gapcosts.gap_costs
+        #end if
+        #if $annotation_options.tax_scope:
+            --tax_scope=$annotation_options.tax_scope
+        #end if
+        #if $annotation_options.target_orthologs:
+            --target_orthologs=$annotation_options.target_orthologs
+        #end if
+        #if $annotation_options.go_evidence:
+            --go_evidence=$annotation_options.go_evidence
+        #end if
+        #if $seed_ortholog_options.seed_ortholog_evalue:
+            --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue 
+        #end if
+        #if str($seed_ortholog_options.seed_ortholog_score):
+            --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score 
+        #end if
+        $output_options.no_file_comments
+        $output_options.no_annot
+        $output_options.report_orthologs
+        --output='results'
+        -i '${input}'
+    ]]></command>
+        <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>
+            </param>
+            <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
+                label="Are these coding DNA sequences that need to be translated?"/>
+            <conditional name="db">
+                <param name="mode" type="select" label="Annotation Type">
+                    <option value="hmmer">HMM</option>
+                    <option value="diamond">DIAMOND</option>
+                </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"/>
+                            <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
+                        </options>
+                    </param>
+                    <conditional name="hmm_options">
+                        <param name="hmm_settings" type="select" label="HMM Search Options">
+                            <option value="default">Use defaults</option>
+                            <option value="specified">Set HMM Search Options</option>
+                        </param>
+                        <when value="default"/>
+                        <when value="specified">
+                            <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
+                            <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" />
+                            <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
+                            <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`.  Default=5000" />
+                            <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
+                            <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases).  Default=40,000,000" />
+                        </when>
+                    </conditional>
+                </when>
+                <when value="diamond">
+                    <!-- db.database is used in diamond mode only to name outputs -->
+                    <param name="database" type="hidden" value="diamond"/>
+                    <conditional name="matrix_gapcosts">
+                        <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
+                            <option value="BLOSUM90">BLOSUM90</option>
+                            <option value="BLOSUM80">BLOSUM80</option>
+                            <option value="BLOSUM62" selected="true">BLOSUM62</option>
+                            <option value="BLOSUM50">BLOSUM50</option>
+                            <option value="BLOSUM45">BLOSUM45</option>
+                            <option value="PAM250">PAM250</option>
+                            <option value="PAM70">PAM70</option>
+                            <option value="PAM30">PAM30</option>
+                        </param>
+                        <when value="BLOSUM90">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM80">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM62">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 11 --gapextend 2">Existence: 11  Extension: 2</option>
+                                <option value="--gapopen 10 --gapextend 2">Existence: 10  Extension: 2</option>
+                                <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 1">Existence: 13  Extension: 1</option>
+                                <option value="--gapopen 12 --gapextend 1">Existence: 12  Extension: 1</option>
+                                <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM50">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                                <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
+                                <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
+                                <option value="--gapopen 9 --gapextend 3">Existence: 9  Extension: 3</option>
+                                <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
+                                <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13  Extension: 2</option>
+                                <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
+                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                                <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
+                                <option value="--gapopen 15 --gapextend 1">Existence: 15  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM45">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                                <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
+                                <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
+                                <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
+                                <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
+                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                                <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="PAM250">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 15 --gapextend 3">Existence: 15  Extension: 3</option>
+                                <option value="--gapopen 14 --gapextend 3">Existence: 14  Extension: 3</option>
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                                <option value="--gapopen 17 --gapextend 2">Existence: 17  Extension: 2</option>
+                                <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
+                                <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
+                                <option value="--gapopen 21 --gapextend 1">Existence: 21  Extension: 1</option>
+                                <option value="--gapopen 20 --gapextend 1">Existence: 20  Extension: 1</option>
+                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="PAM70">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
+                                <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="PAM30">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
+                                <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 5 --gapextend 2">Existence: 5  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9  Extension: 1</option>
+                                <option value="--gapopen 8 --gapextend 1">Existence: 8  Extension: 1</option>
+                            </param>
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
+        <section name="annotation_options" expanded="false" title="Annotation Options">
+            <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
+                <option value="NOG">All organisms  (NOG)</option>
+                <option value="aciNOG">Acidobacteria  (aciNOG)</option>
+                <option value="acidNOG">Acidobacteriia  (acidNOG)</option>
+                <option value="acoNOG">Aconoidasida  (acoNOG)</option>
+                <option value="actNOG">Actinobacteria  (actNOG)</option>
+                <option value="agaNOG">Agaricales  (agaNOG)</option>
+                <option value="agarNOG">Agaricomycetes  (agarNOG)</option>
+                <option value="apiNOG">Apicomplexa  (apiNOG)</option>
+                <option value="aproNOG">Proteobacteria_alpha  (aproNOG)</option>
+                <option value="aquNOG">Aquificae  (aquNOG)</option>
+                <option value="arNOG">Archaea  (arNOG)</option>
+                <option value="arcNOG">Archaeoglobi  (arcNOG)</option>
+                <option value="artNOG">Arthropoda  (artNOG)</option>
+                <option value="arthNOG">Arthrodermataceae  (arthNOG)</option>
+                <option value="ascNOG">Ascomycota  (ascNOG)</option>
+                <option value="aveNOG">Aves  (aveNOG)</option>
+                <option value="bacNOG">Bacilli  (bacNOG)</option>
+                <option value="bactNOG">Bacteria  (bactNOG)</option>
+                <option value="bacteNOG">Bacteroidia  (bacteNOG)</option>
+                <option value="basNOG">Basidiomycota  (basNOG)</option>
+                <option value="bctoNOG">Bacteroidetes  (bctoNOG)</option>
+                <option value="biNOG">Bilateria  (biNOG)</option>
+                <option value="bproNOG">Proteobacteria_beta  (bproNOG)</option>
+                <option value="braNOG">Brassicales  (braNOG)</option>
+                <option value="carNOG">Carnivora  (carNOG)</option>
+                <option value="chaNOG">Chaetomiaceae  (chaNOG)</option>
+                <option value="chlNOG">Chlorobi  (chlNOG)</option>
+                <option value="chlaNOG">Chlamydiae  (chlaNOG)</option>
+                <option value="chloNOG">Chloroflexi  (chloNOG)</option>
+                <option value="chlorNOG">Chloroflexi  (chlorNOG)</option>
+                <option value="chloroNOG">Chlorophyta  (chloroNOG)</option>
+                <option value="chorNOG">Chordata  (chorNOG)</option>
+                <option value="chrNOG">Chromadorea  (chrNOG)</option>
+                <option value="cloNOG">Clostridia  (cloNOG)</option>
+                <option value="cocNOG">Coccidia  (cocNOG)</option>
+                <option value="creNOG">Crenarchaeota  (creNOG)</option>
+                <option value="cryNOG">Cryptosporidiidae  (cryNOG)</option>
+                <option value="cyaNOG">Cyanobacteria  (cyaNOG)</option>
+                <option value="cytNOG">Cytophagia  (cytNOG)</option>
+                <option value="debNOG">Debaryomycetaceae  (debNOG)</option>
+                <option value="defNOG">Deferribacteres  (defNOG)</option>
+                <option value="dehNOG">Dehalococcoidetes  (dehNOG)</option>
+                <option value="deiNOG">Deinococcusthermus  (deiNOG)</option>
+                <option value="delNOG">delta/epsilon  (delNOG)</option>
+                <option value="dipNOG">Diptera  (dipNOG)</option>
+                <option value="dotNOG">Dothideomycetes  (dotNOG)</option>
+                <option value="dproNOG">Proteobacteria_delta  (dproNOG)</option>
+                <option value="droNOG">Drosophilidae  (droNOG)</option>
+                <option value="eproNOG">Proteobacteria_epsilon  (eproNOG)</option>
+                <option value="eryNOG">Erysipelotrichi  (eryNOG)</option>
+                <option value="euNOG">Eukaryotes  (euNOG)</option>
+                <option value="eurNOG">Euryarchaeota  (eurNOG)</option>
+                <option value="euroNOG">Eurotiomycetes  (euroNOG)</option>
+                <option value="eurotNOG">Eurotiales  (eurotNOG)</option>
+                <option value="fiNOG">Fishes  (fiNOG)</option>
+                <option value="firmNOG">Firmicutes  (firmNOG)</option>
+                <option value="flaNOG">Flavobacteriia  (flaNOG)</option>
+                <option value="fuNOG">Fungi  (fuNOG)</option>
+                <option value="fusoNOG">Fusobacteria  (fusoNOG)</option>
+                <option value="gproNOG">Proteobacteria_gamma  (gproNOG)</option>
+                <option value="haeNOG">Haemosporida  (haeNOG)</option>
+                <option value="halNOG">Halobacteria  (halNOG)</option>
+                <option value="homNOG">Hominidae  (homNOG)</option>
+                <option value="hymNOG">Hymenoptera  (hymNOG)</option>
+                <option value="hypNOG">Hypocreales  (hypNOG)</option>
+                <option value="inNOG">Insects  (inNOG)</option>
+                <option value="kinNOG">Kinetoplastida  (kinNOG)</option>
+                <option value="lepNOG">Lepidoptera  (lepNOG)</option>
+                <option value="lilNOG">Liliopsida  (lilNOG)</option>
+                <option value="maNOG">Mammals  (maNOG)</option>
+                <option value="magNOG">Magnaporthales  (magNOG)</option>
+                <option value="meNOG">Animals  (meNOG)</option>
+                <option value="metNOG">Methanobacteria  (metNOG)</option>
+                <option value="methNOG">Methanococci  (methNOG)</option>
+                <option value="methaNOG">Methanomicrobia  (methaNOG)</option>
+                <option value="necNOG">Nectriaceae  (necNOG)</option>
+                <option value="negNOG">Negativicutes  (negNOG)</option>
+                <option value="nemNOG">Nematodes  (nemNOG)</option>
+                <option value="onyNOG">Onygenales  (onyNOG)</option>
+                <option value="opiNOG">Opisthokonts  (opiNOG)</option>
+                <option value="perNOG">Peronosporales  (perNOG)</option>
+                <option value="plaNOG">Planctomycetes  (plaNOG)</option>
+                <option value="pleNOG">Pleosporales  (pleNOG)</option>
+                <option value="poaNOG">Poales  (poaNOG)</option>
+                <option value="prNOG">Primates  (prNOG)</option>
+                <option value="proNOG">Proteobacteria  (proNOG)</option>
+                <option value="rhaNOG">Rhabditida  (rhaNOG)</option>
+                <option value="roNOG">Rodents  (roNOG)</option>
+                <option value="sacNOG">Saccharomycetaceae  (sacNOG)</option>
+                <option value="saccNOG">Saccharomycetes  (saccNOG)</option>
+                <option value="sorNOG">Sordariales  (sorNOG)</option>
+                <option value="sordNOG">Sordariomycetes  (sordNOG)</option>
+                <option value="sphNOG">Sphingobacteriia  (sphNOG)</option>
+                <option value="spiNOG">Spirochaetes  (spiNOG)</option>
+                <option value="spriNOG">Supraprimates  (spriNOG)</option>
+                <option value="strNOG">Streptophyta  (strNOG)</option>
+                <option value="synNOG">Synergistetes  (synNOG)</option>
+                <option value="tenNOG">Tenericutes  (tenNOG)</option>
+                <option value="thaNOG">Thaumarchaeota  (thaNOG)</option>
+                <option value="theNOG">Thermoplasmata  (theNOG)</option>
+                <option value="therNOG">Thermotogae  (therNOG)</option>
+                <option value="thermNOG">Thermococci  (thermNOG)</option>
+                <option value="treNOG">Tremellales  (treNOG)</option>
+                <option value="veNOG">Vertebrates  (veNOG)</option>
+                <option value="verNOG">Verrucomicrobia  (verNOG)</option>
+                <option value="verrNOG">Verrucomicrobiae  (verrNOG)</option>
+                <option value="virNOG">Viridiplantae  (virNOG)</option>
+            </param>
+            <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
+                <option value="one2one">one2one</option>
+                <option value="many2one">many2one</option>
+                <option value="one2many">one2many</option>
+                <option value="many2many">many2many</option>
+                <option value="all" selected="true">all</option>
+            </param>
+            <param name="go_evidence" type="select"
+                    label="Select the set of GO terms that should be used for annotation">
+                <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
+                <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
+            </param>
+        </section>
+        <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
+            <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
+                <help>
+                Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. 
+                Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
+                </help>
+            </param>
+            <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
+                <help>
+                Min bit score expected when searching for seed eggNOG ortholog. 
+                Queries not having a significant seed orthologs will not be annotated.
+                </help>
+            </param>
+        </section>
+        <section name="output_options" expanded="false" title="Output Options">
+            <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
+                label="Exclude header lines and stats from output files"/>
+            <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
+                label="Skip functional annotation, reporting only hits"/>
+            <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
+                label="Output a file with the list of orthologs for each hits"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
+            <actions>
+                <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
+            </actions>
+        </data>
+        <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
+            <filter>not output_options['no_annot']</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>
+            </actions>
+        </data>
+        <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits"  from_work_dir="results.emapper.hmm_hits">
+            <filter>db['mode'] == 'hmmer'</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
+            </actions>
+        </data>
+        <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs"  from_work_dir="results.emapper.annotations.orthologs">
+            <filter>output_options['report_orthologs']</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="query_name,orthologs"/>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <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="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="no_annot" value="true"/>
+            <param name="mode" value="diamond"/>
+            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+eggnog-mapper
+=============
+Overview
+--------
+
+``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. 
+Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. 
+The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, 
+as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
+
+EggNOG-mapper is also available as a public online resource:  `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
+
+Options
+-------
+
+``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_. 
+HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences. 
+
+
+Outputs
+-------
+
+**hmm_hits**
+
+For each query sequence, a list of significant 
+hits to eggNOG Orthologous Groups (OGs) is reported. 
+Each line in the file represents a hit, where evalue, bit-score, 
+query-coverage and the sequence coordinates of the match are reported. 
+If multiple hits exist for a given query, results are sorted by e-value.
+Only returned when using HMMER mode. 
+
+**seed_orthologs**
+
+each line in the file provides the best match of each query within the best Orthologous Group (OG) 
+reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. 
+The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. 
+If using the diamond search mode, seed orthologs are directly 
+obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
+
+**annotations**
+
+This file provides final annotations of each query. Tab-delimited columns in the file are:
+
+- ``query_name``: query sequence name
+- ``seed_eggNOG_ortholog``: best protein match in eggNOG
+- ``seed_ortholog_evalue``: best protein match (e-value)
+- ``seed_ortholog_score``: best protein match (bit-score)
+- ``predicted_gene_name``: Predicted gene name for query sequences
+- ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
+- ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
+- ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
+- ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
+- ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
+- ``COG functional categories``: COG functional category inferred from best matching OG
+- ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkv1248</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r f4e5279b5d10 test-data/DIA_nlim.emapper.seed_orthologs
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DIA_nlim.emapper.seed_orthologs	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,1 @@
+Nlim_1033886738.Nlim_1033Cytidyltransferase-like	886738.Nlim_1033	5.4e-20	78.6
diff -r 000000000000 -r f4e5279b5d10 test-data/HMM_nlim.emapper.hmm_hits
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMM_nlim.emapper.hmm_hits	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,1 @@
+Nlim_1033886738.Nlim_1033Cytidyltransferase-like	ENOG411CB2I	2.3e-16	46.1	39	1	39	1	38	0.948717948718
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1439
+MKIQIYILIGVVVLTLISVGIMTNQDQNTHENKIRVAYFPNISHAIPIVGIEKGFFSNHIGSDIDIQPILFDSGPQVIESIFAGSVDIAYVGPGPAINAFLKSEQHDVKILSGAASGGVSFIVHPKSEIKSVADFAGKRIAAPQIGNTQDISLRTYLSDNGLKPAEKGGSVIILNTGNSDIYILFAKGDIDGAWVPEPTATILVQQLGGTRLFNENELWPENKFATVVLIAKEEYVNSHPEIIQKWLEAHQQTADWINSNKEETKTIFFDFMKNEMGKSLPVELIDESLSNLEITSDPIVSSIDTIAKRADSLGYLGRHGYNLDGLFFDKNSNSQSQEVLVNNDQT
+>436308.Nmar_1285
+MKIRSVIAAGIGAIIVFSALGIALSSSDTTYENKIRIAYFPNIGHAIPIVGMEKGFFAEHLGDDVKIETKVFDSGPQAIESLFANSIDIAYVGPGPAINGFLNSNNQNVKILAGAASGGASFIVHPDSEINTADDFAGKKIAAPQIGNTQDVSLRHFLAENQLKPAEKGGNVVVYNIPNPDIYTLFVKGDIDGAWVAEPWATILETELDGKRLFHEEELWPDKEFASVLLIGNVDYIDKNSVVWADYIRAHHETQIWIESNPIETRNVFNDFLDSYLGQSLSDDVVDVALSNIMITADPKPNSVVSFAEKADTLGYLGRNGYDLSGIFYSFDTNSLEEAST
+>886738.Nlim_1020
+MKMRSIILAGIASIILILSVGIIVNTDGSTRENKIRVAYFPNITHVVPIIGLERGTFANEIGNTITIQPILFDSGPQVIESIFAGSVNIAYVGPGPAINGFLKSEHHNVKILSGAASGGVSFIVHPDSKINSAEDFIGKRIAAPQIGNSQDISLRTYLSANGLKPAEKGGSVIVLNVPNSDIYTLFAKGDIDAAWVAEPTATLLVQKLNGTRLFDEIDMWPDQKFASVLLIANEDYVNQHPEVIRKWLEAHQQTIDWINSNPEETRIIFNQFLKRELGKSLPDNLIDESLSKLQITSDPIVSSIETFAKRADSLGYLGRHGYSLDGIFFDINSNSQLQEVLIP
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_0167
+MSYDGAIEALSTDALKFVKDDFVIGLGSGRAATAFVKSLSSFIKIKNYNIRGVPTSLQIKLIAEKGGIPLVEAEQVDHIDIVFDGADQIDSQKFVIKGGGGALLRENILFNLAKKVVVMADKSKFVKNFTRSVPVEVHPQARNLVTYEIKKLGGKAELRLIDRGYPFFTENGNIILDCDFGVIKNPKILSQKIKQVAGVIESGIFIRKPDVIYRAKTGGKFDII
+>436308.Nmar_0218
+MSYDGAITALSNNALKFVKDDYVVGLGSGRAATVLVKSLGKLIKLKNYNIKGVPTSLQIKLIAEKVGIPLIEADQVEHIDVVFDGADQIDSQKFVIKGGGGALLRENILFSLAKKVVVMADKTKFVKNFTRTVPVEVHPLARNSVSKSMKKLGGKAELRSLDRGYPFFTENGNIILDCDFGTIKNPKALTQKIKATTGVLESGIFLRKPDVIYRAKTGEKFDIL
+>886738.Nlim_1248
+MSYDDAIEALSTDALKFVKDGFVIGLGSGRAATSFVKSLSSFIKIKNYSIKAVPTSLQIKLIAEKGGIPLVEADHVEYIDVVFDGADQIDSQKFVIKGGGGALLRENILFNLSKKVVVMADKSKFVKNFTREVPVEVHPLARNSVIDAIRKLGGNAQLRSLDRGYPFFTENGNIILDCNFGTIKNPKSLTQKIKQITGVMESGIFLRKPDVIYKAKTGGKFEII
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+>1001994.MY1_1435
+MVQKEPFLTALQNRILLFDGAMGTEIQKYNPKPEDFPNNQDGFNDGLVITHPDWIKKIHKNYLDAGSDCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLAVEVCSEYTDKPRYVIGSMGPSGYLPSSNDPDLGQKPLGEIRNAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHNAMKKTGKKVPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGLNCSTGPAEMTPSVRWLDEQNEHNLLVVPNAGMPENQGGQAVYKMTPQKMGELLGDFLKQYKKVRIIGGCCGTNPEHIAVLRKVIDEKAYSVKG
+>436308.Nmar_1268
+MTEKEPFLDALQNRVLLFDGAMGTEIQKFNPKPEDFPNNQDGFNDGLVVTRPDWIKQIHRHYLDAGADCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLASEVCQEYSDRPRYVIGSMGPSGFLPSSNDPDLGQKPLDEIKEAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHQAMEKTGKKIPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGMNCSTGPIEMTPSVRWLDEQNEHNILVVPNAGMPENEGGQAVYKMTPEKMGDALGDFLNQYKKVRIIGGCCGTNPEHIKVLRKVIDEKANSVEG
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_0571
+MDKSGVIVGAISGAAIVAIIFAVILAVPPTAVKADVISDNKSIPSATGAILTDYSKKLSLIEIFEKSEPGVVRINVQRAEQSNGTSGVGSGFVFDKQGHIITNAHVVKNVKKVVVTFLDGRSYNAEIVGSDQYTDIGVIKVNADLSLLQPLPLGDSANLKVGEPIAAIGNPFGLSGSMTSGIISQLGRLLPSGAGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTLAKIVPKIIVDGKYIHPWIGIAGRDIDPDLAKVLNLNDAVGFLVITVVDDSPAAKAGIHGSNETVEVDGIKYLIGGDIILSVDGNQVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTNIIITLDERPNGN
+>436308.Nmar_0594
+MDKSGVFVGGAIGAVIVVAIFAVLFVSPPESVKPDIVVSNGHGPSTVGEVTPVYSKDLSLIEIFEKSEPGVVRVNVQREEVSDVGGVGSGFVFDKQGHIITNEHVIDDAKKIIITFLDGRSYNAEIIGTDEFTDLAVVKVNADLALLHPLSIGDSSNLKVGEPIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSATGEFTGVGFAIPSQTVAKIVPTLIEDGDYKHPWIGISGRDIDPDLAKVLELPDAVGFLVVTVIEDSPASKAGLIGSEKTIDVDGVNYPMGGDIILAVDGIEVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTDISIILQERPNGN
+>886738.Nlim_0162
+MSKSEMLVGAAIGASVVAVIFAIILISPAAITKSEINTSDKSIPSVTQTAPAYSTNLSLIDIFEKSEPGVVRVNVQRTDQSNGTSGLGSGFVFDKKGDIITNAHVVKNAKNIVVTFLDGRSYNADLIGSDEFTDIAVIKVNADLTRLHPLSLGDSSSLKVGESIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTIVKIVPSLIQDGTYHHPWIGITGRDIEPDLAKVLKLNDAVGFLIVSVIDDSPAAKAGLHGSNETVQVDGLNYQIGGDIILSVDGKQVRKIDDILVHLQRAKSVGDEMVLEILRDGRTTNITINLEERPNGN
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1525
+MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVSKSLSTEPWDGYPNPTIFGINGGGWINAVGLSNPGAPNFAKMIEPNKDVPIIISLVGSIPEDFSTMVEQFKNSKVIAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTNVPVIAKVGLGTTHYLNTVSAAIDSGIDAITAINTIRAIAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDALEFILAGASAIQIGSAIGDNWIHVFNDINKGILQYMKRKGYSKIDEMIGLAKKS
+>436308.Nmar_1390
+MEPNLATSIGPIQLDRPVMLASGILGISLDVFSRLYRSGAGAVVTKSLSTEPWEGYPNPTIFSVKGGGWINAVGLSNPGAENFAKMIEPNQDVPIIVSLVGSIPEDFEKMIKQFENCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVTTVKNSTNVPVIAKVGLGTTHYLNTVGTAIESGIDAITAINTVRSMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAVEFFLAGASSVQLGSAIGDNWIDVFNEINTGILQYMEKKNYSKIEEMIGLAKKS
+>886738.Nlim_1764
+MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVTKSLSTEPWDGYPNPTIFSVNGGGWINAVGLSNPGAPNFAKMIESNTTVPIIVSLVGSIAEDFEMMVSQFKNCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTAVPVIAKVGLGTTHYLNTVKTAIDSGIDAITAINTVRAMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAIGDRWLNVFNDINDGIIRYMKRKGYSKLDEMVGLAKKS
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_0238
+MLEISSTPLVIIAILGTVGILLPIISIARKEKGSNSFYAVIAFAALIVSIGYVAYQFVNGNILPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTVGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLAGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYHILNHAVMKGMAFIAVTGIITTLAVTHIDKLKGLGRRMPITALGLIISLFALAGVPPLAGFWSKLVLFGGALDAGTSIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGENEKRVSEPKSIIAIMIFSIVFLVGFGIYPDPIIKFVEFAAPTFSLGVMP
+>436308.Nmar_0286
+MLEITSTPLILIAILGTVGVILPIISIARKEKGSNSFYAVIAFAALIVSMAYVGYEFINENVAASALFSDDVIVDDAFGGFFAIAMLIVALFTTVGSFNYMRKHNSPAVYYSLILLATIGMILVAYSTDLVMLFVAWELMSIPTYILVGYMKKNPSSNEAALKYFLFGALSSAIIVYGIAISYGLTGSTNIGEVIEGYSTLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPSPVTALLAAATKKAGFAAAIRIIVLGMMALNLDWTLALGIIAVMTMTIGNVAAIMQKNLSRMLAYSSIAHAGYILIGLAVAPYSSLGLQGSLYQIFNHAVMKGAAFIAIAGIVTTLAVTHIDKLKGLGRRMPITALGMVISLFALAGVPPLSGFWSKLMLFGSALDASTALWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVSEPKSIVAVMIFSIIFLVGFGVYPEPLLKFVEFATPVVSLGLMP
+>886738.Nlim_1181
+MLEITSTPLVIIAILGTVGVLLPIISIARKEKGSNSFYAIIAFAALIVSIGYVAYQFINDNVLPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTIGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLVGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDASLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYQILNHAVMKGMAFIAVTGIVTTLAVTHIDKLKGLGRRMPITAFGLVISLFALAGVPPLAGFWSKLMLFGGALDAGSTIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVREPKSIIAIMVFSIIFLVGFGVYPDPIIKFVEFAAPTFSLGIMP
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1852
+MISLNRFVIILIVGIFVSGILTISFISNSYVDANSTKKINFTKTIISSQDPGQGHENHQLSLILSPNEGTLYDGSMTFTSNEPVDVVVLHEITGNDVKGQPTWTIDGKTIYAMSLIDLKSKSDSFEFTGAALALHSSNSKEFTATVSVDGWIRGQPTEVIMQKIQVEKDPSLMLSRANVEATMPMHEGLYKGNSIFYIITDTSREEYSKKITEKQDWKVQTSTLIEKMPEEILQKIFIFNNGVRGQGIYGHQKEIFSSTPVQESKYSALNSVIEVSWKKGQNAKVLESFEDVIDAEKNGRIEFTKTGVVINSPQIIWPNGQMLVRNDTKITDDLTFSGGQITKINKDEMTVTFVAHRMWGPDGKTIYAIVTDATPSNPSEIMGIPFSPVYDNLITNSSAADLFQFQNGIKGSGSLGYQPGITSVNSDQENYSPIWRIYNVEWHNPKDAKILQTMSDIDSFKAKDLISVSLARPMNSHHIINGPLIDPFQ
+>436308.Nmar_1753
+MLRKLIAILIIGIFATSIITASSLSDQFADAGSRKKIHFTQTFTSSQDPGQGHENHQLSLILSPNQGTIYDGSMTFTSSEPVQIVVLHEINSDDAKGQPTWSIDGNTVYGLSLIDLQEKSGSFEFTGAALGLHSPNSKQFTSTVSVDGWIRGQPTEVIMQKIELEKEEPMSLLSRANVPATIPIHEGIYGGEKVLYIITDGSDEEYARELSEKQEWNVELAPVLADVPEDALQKIFVFKNGVKGEGLYGFQNEIFSSTPQQESEYSALSSVIEVTWKTGQKEIVFESANDVIAAEENGRIEFDETGVVLNTPHIVWPGGQMQVRADQEIADDMPYGGGQITEINEEEMTVTFVAHRGWGPDGRTIYYIVTDATPFGPAEMMGVTSSPTSANLIAHSGAVDLFQFKNGIKGTGPLGFQAGIAAASLGDENYSPMWRIYLIEWNDSENAKILETKSDIDSFRADDLITVSITRPTNSDHIVNCPFIDPFQ
+>886738.Nlim_1479
+MNRFTIILIVGIFIIGALTVSFVSDNYVNANSTKKINFTKTITSSQDPGQGHENHQLALILSPNQGTLYVGSMTFTSSEPVEIVVLHEINNDDVKGQSTWTIDGKTVYAISLIELKAKSGSLEFTGAALALHSTNSKEFTATVSIDGWIRGQPTEVTMQKIQVQQNPPLELSRANIAASIPMHEGFYDGKSVFYIITDSSQKEYAEMITKKQNWKVEVAPEIKKISENTLQTIFIFKNGVNGDGIYGRQKEVFSSTPSQVQKYSALNSVIEVTWKKGQNASTLESYEDIINAEKNGRIEFSKTGIVINTPQIIWPDGQMLVRNNKEITNNLKFDGGQITEINKDEMTVTFVAHRGWGPDGKTIYYIITDTTPSGPAKIMGIPFSPVSEHLITNSSKSDLYQFKNGIKSSGSLGYQAEIISVMPGDDSYSPIWRVYNIEWNNPENASILETISDITSSKIKDLILVSLARSMNNQYVINGPIIDPFQ
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+>436308.Nmar_0483
+MTALATKSENIEKQIISDPSDTIDSEKYKMIAENVTISYDGIQAVKNITMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVDGKVMIDNIDLYDQSIDPIYHRRKVGMVFQKPNPFPTMSIYDNVTAGLKLNGVKDKRILDEIVEDSLKMAYLWDEVKGDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETITELKKEYTIIIVTHNMQQAVRVSDYTGFMYLGDLVEFRETKKLFTDPKNELTAKYVQGQFG
+>886738.Nlim_0922
+MTAMTTKPTHAETSFTSKSQPTLDSDKYKMIAENITVSYGGVDAVKNVTMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVTGKVMIDNIDLYAKDIDPIYHRRKVGMVFQKPNPFPTMSVYDNVTAGLRLNGVRDKRILDEIVEDSLKMAYLWDEVKNDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETIIELKKDYTIIIVTHNMQQAIRVSDYTGFMYLGDLIEFRETKKLFTDPKDDLTAKYVQGHFG
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1452
+MELIEKIILTQIYLSGITGKSYKDNLKTKKGFTENIINSKIDELVKNKLITEDKSALTELGRSSLRVVLAGGVFDIIHPGHIHTLNAAKILGDVLVVVVATDNTAIKMKKRQPLHSKEQRQELVNSLSMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIEGCKKINLDAKVARLQSPIPESSSSKIQKEYGESIHGI
+>436308.Nmar_1298
+MLEQSQRTILSTIYVCQIEGTNPIEKIKRKTAFSDDQINSKIEELIKKQLVNEDKKTLTESGRDSLKVVLAGGVFDIIHPGHIHTLNAAKELGDALVVVVATDNTAVKMKKRRPLHSQEQRQELVNSLSMVDLCLIGQEDDIFKTVNNVRPQIIALGYDQAHQEKFITEGCKKINLDAKVARLQSPIPDSSSSKIEKEYGESIHGI
+>886738.Nlim_1033
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLEIDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHPGHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKEQRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQKEYGESIHGI
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1646
+MSCSGEIVDEEKLIQIKPGILQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMEPEKVSEPKEILTKLMEERKKLIMGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEATKSIFLVTNGQEPDMIQRLQDKDALPTQLYLSTNAADYDSFLKINRPKYDDSWQRWNRTLEMLKHLDTRTVLRITLIRNYNDQKEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRRFSEEVAKHSEIFSIMDESLVSRIVILQNNQRSINRWISAYSNTN
+>436308.Nmar_1529
+MSCSGEVVEEEQLIQIKPAISEQLKKAKYGVSDHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLEMKPEQVAEPEEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLNSLEATKSIFLVTNGQEPDMIQKLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWERWNRTLGMLKHLNTRTVLRITLIRNYNDQKSMIPAFAKMFKEASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVKRFSEQIAKQSQIFSVMDESFVSRISILQNNERFIDRWIPAYVNTN
+>886738.Nlim_1932
+MSCSGEIVDEERLIQIKPGISQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMDPEKVAEPKEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEETKSIFLVTNGQEPDMIQRLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWQRWNRTLEMLKKLDTRTVLRITLIRNYNDQEEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRKFSESVAEHSQIFSVMDESLVSRIVILQNNQRTIDRWIPAYANTN
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+>436308.Nmar_0061
+MPNFDKTWARQETQSVTGKLREAVKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNTMTQTLNGLMMDSLAGDSFNMESDVSSEETEKILQEASAVAEQQIGDKFPSVPSSTGLSSGTSTSTFE
+>886738.Nlim_1611
+MPNFDKTWARQETPGVTEKLRETIKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNSMTQTLNGLMMDSLAGDSFSMETGASSEETERILQEASAVAEQQIGDKFPSVPTSTGLSQSSQSTY
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_0188
+MLSTGMWVEKYRPSKLSEIVNQKEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCISRQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMVDVPFKIIILDEADEMTSDAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPEEDVINHLENIAKKEKVKSDKKGLKAIYDYSEGDLRHAINLMQATASIGEISEENVKSSAGLTKTSDVDIVLKMALSGKIVDAREKMIELTKVYGMSESDFLKYLNSAVFKIKHDNISDILEVIAKYDYRILVGANPEIQLTAMLAELGKLEK
+>436308.Nmar_0240
+MAATGMWVEKYRPMKLSEVVNQTEIIGSLEALIKDPTDMPHLLFSGSAGVGKTTTALCISRQILGDYAKDYTLELNASDERGIGMVREKVKKFSRYAGMADVPFKIIILDEADEMTSDAQTALRRIIEDTAKICRFILIANNISKIIDPIQSRCATFKFTAVPEEDVIKRLEEIAKKEKVKADKKGLKAIYDYSEGDLRHAINLMQATASLGSISEDNVKASAGLTKTTDVDEVLKIALSGKVPEAREKMIELIKVYGMSESDFLKYLNSAVFKSKHDKLSDILEIIAKYDYRILVGSNSEIQLSAMLAELAKVEN
+>886738.Nlim_1226
+MLSTGMWVEKYRPTKLSEIVNQTEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCIARQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMAEVPFKIIILDEADEMTADAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPQEDVINHLESISKKEKIKSDKKGLKAIYDYSEGDLRHAINLLQATASLGEVTEENVKASAGLTKTSDVDEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKYINSAVFKTKHEKLSDILQVIAKYDFRILSGANSEIQLSALLAELSTLK
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_0435
+MNKVNLNIKQRKIISDKIFKIGVTTAGAYVLIVVVLIAFQLVSESYPVWEEEGLSFITKTDWNAVEGRESFGALPYILGTLTTSAIAMMIGVPLSIGIAMFISDAPPKIGAPLGFLVELLAAVPSVIYGLWGLYVFRIYFRDWFETPLHDAFGDNIWLFSGNPYGLDILTASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAIFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGLGAIPSSLFGPSQTMSSIIANEFVEASPASIHMPALIGIGLILLLIAIVINVVAHLLVTRMLKIKEGAINN
+>436308.Nmar_0481
+MGRPKLNPPKVGRRPISDKIFKVGATVAGVYVLVVIVLLAFQLISESAPIWDEYGLSFIVKSEWNAIDDRQDFGVLPYIFGTLVTSALAMVIGVPLSIGIAMFISDAPSKIGGPLGFLVELLAAVPSVIYGLWGLFVFRVYFVDWVEKPLHNTFGDSIWLFSGTPFGLDILTASVILAIMIIPTVSAVSREVMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGPNAFADSLFDPSQTMSSIIANEFNEASLGTLHLPALIGVAVVLLLIAIAINVVAHILVTRMLKVKEGAINN
+>886738.Nlim_0924
+MISDKVFKIGATVAGTYVLVVVVLIAFQLISESYPIWEKEGLSFITSTDWNAVEGRESFGALPYIIGTLTTSAIAMAIGVPLSIGIAMFISDAPAKIGGPLGFLVELLAAVPSVIYGLWGLFVFRIYFRDWIETPLHNAFGDNIWLFSGNPYGLDIITASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGIGAIPSSLFGPSQTMSSIIANEFVEASPASVHMPALIGIGLILLLIAIVINVIAHLLVTKMLKIKEGAINN
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+>1001994.MY1_1290
+MTPSELNEEKLVEIPAEHTFSELYDDVKYDPDIRPGRELQERDSLHEVLLKRRLRQKLVELNPGNPDIVYDIAVQKIELISEPTLIETNRAFHQMLLSGIKVAYQEDNQTKYSVMKLIDFDNPEKNDFIAVRQFLLVQHEERRLDHVIFVNGIPLIILEYKSMADKNATIVDAFHQLGKTKYQRDIPIIFRYNAFLVISDRLNAKYGTINAPFERFSDWNDLTQPDKKVANRLEILQKLLLNKTTILDVIKNFIEYESDGKNLIKKICQQHQYHAVNTIVKKTSDVYSQQGENRIGVVWHTTGSGKSLTMIYYVNSLSQIEKFENPTFIIITDRRDLDEQLNHFFRIAGFPYPKPETAILEADSILDLREKLQVPSGKIIFTTIQKFQTTEEEREGKVKYPKISDRRNIIIIADEAHRSQYKKMAQNLQTALPNALRIGFTGTPIELEDRSTTQVFGDIISSYKIPEAVRDGATVQISCETHPVTLLLLNKFIGKDFEEITQGLDEENVTTLARRGAEFTKLVEDPDRIKTIANDIVSHFNKKQKIFKGKAMIATSTKLAAARFADYISSLKVAPECTCIVSGATSQKPESTPEKRTREAIIQKHYKDKLTIENILTRFKDENDPLSLLIVCDMYLTGFDAPLIHTMYIDKPLRDHNLIQAISRVNRVWKNKPGGAIIDYIGIADDLDRAFSAYAQDDVKGAMIPTAEIIEIMKKKHSDLINFFDPKISNRQGLDESQELQLIYDAIDEIVYDDIVKREFIKIVTELTKAYAVCTPHPSCLDVEDDLRFFQKLRKILLKATSNVPVDLTEMESAISDLVEQGIGADQVVKGFKISFDPKKQDISKEYLNDIKKLKQKNLKAELAYKLLDDAIQAKFKRNLVKRKSFQDRIEEALSKYHARFWDNDDTIQKLEEVGKEITNESSREQELGLNDEEIAFYDVVSLGKDYVKSDAVIKQISLDLTKYLKGNIRIDWINQENIKAEIRMGVRKILLRADFPTDKIEEIVPKIMDQAETNYG
+>436308.Nmar_0608
+MNFRIEDNEEGRQVELPALELITALGYTYIPNYELNIPKERPDHRQVLLYPRLRAAIKRLNDFDDDGIEQAIAQIHEDNFPIGMPMIDANEKIRIKLTGRAGENAIAQPITIKQYGKKGIEYPTVKFFDFDPKKIGTKEDKNEYLVTNQFKHLGNRTEIECDIVIFVNGIPLVLIECKKPTTIDLMKTVWKENLEKYQRDGSHSLGHEKLFFFNHVIMATSAIQARYGTLKALPNKYAKWTSLTNITTKELEKLVGRKPTPQDIMLAGMIKKETLLDMLKNFVLYEIEEHKKIKKVAKHQQYRVVTKSVDRISHHKKVEDKGGVIWHTQGSGKSLSMVWFATQLYYKFSRPTIMVITDRRQLNKQIFDTFRNCGFPEPEKPRNRSQLAKTLQYSKGKTIMVNLQKFDKPEKFVETKEKIYVLVDEAHRSQYKWTAGYMRKAMPNAVFFAFTGTPLDRENKNTYRRFGPLIDKYSFTESKEDGATVKVEHMGLLPEIEIEGGNSLNNIFDNLFGHLPKAQQAEIRRKYATKKKIASSPARIRKICEKIVDHYTKKILPNGYKAMIVAPTRAAAVTYKRELEDLTKLPARIIMDSKKDEVGPDEFSWADYYLPQNEALKKAEEFTNPDDPTKFLIVVDMLLVGYDAPIVQVMYLDRPLREHALLQAIARVNRIYDEHKDRGFIIDFWGVTRDLQNALKMFEEQDVQGALDNVDDDLLELDVRHKDFMEKIQGIDSKDHNEIAKRFEDEDEQEEFEYAFKRFAKALEAVLPDKEAVPYEKDLKKGYEIRGKIRAWFYGDRADLSEYGKKVQKIIDKHIRAIGISEISGSKEITYDNFLGFIAKFKGDNRAKAALIKKRATLVIREMSPDNPAFYQKLKERLEKLIQDEKERRVDDAQYFEGIRDIFEEALSGPEKLQKQTGIKDRFQLAIYMLLEEKHSDLKQNKKYSEEIFKKVKKAASVKDWRDKEPQENEIELAVIDTLDKKIFDEKTRDKLASEVYKMAVNNNEW
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1750
+MDRKILGISGGIAVIIAIVAVMLLTPNLESTPIQKHNEKIGLVINAPHSAISLQDLNQIYAEASSTGIGRSNVYMFWNIVEPVRGEYDWKQSDVLMSFNKNNNLKVTLFFSVINGETLGPFPNWIGKPSLNAIGEDRLVNVLDAILSRYDIIDTVVIAGETESQFRYHEQNIPVYKELFNGVYAKLKEKHPDVQIGNGFALHNVLNKNLEHIVSDLAIGDFVAFSYFPVDTLNDIVKTPEEAKADLQKTFEIIPDKKIGLFEVSWSTSDFVGGNETSQQIFLEKSFEFYTENESKIEFFTWYRQYDRPDGTCVIDKPEIANQTLTVGGGSGLGSSEYIMERLSHYICNSGLLDVDGTPKSSWNEFKNQIELIN
+>436308.Nmar_1626
+MDKKILGVGIGVAVVIAIIAGVLSIPSDSNPEVTPVKTNEKIGLVINSPNQSVTLQELDEIYSTASESGIGRSNVYLFWNLIEPEHREYNWQYSDALMSFNQKNDLKVTLYFSIINGETLGPFPDWIGKPPIQSLNEDRVVSVLDAILSRYHIVDTVILAGETESQFRYYEQNIPPYKELFVGVYDKIKEKHPDVKIGNAFALHQVLNKDLQNIVTDLDVGDFVAFSYSPVDTVGDMVKTPQQAKEDLEQIIDLAGDRNAAIFEISWSTSDFVGGSEESQTEFLEKSFEFYAENESELEFFTWYRQNDKPEGTCAFEVQEVGEDKLTVGGSGFGSSEHVIERLDHYVCNAGLFDENGNPKSGWNEFKNQIQMLN
+>886738.Nlim_1388
+MDKKILSIGIGIAIVIALVLVVIGFQSAEIITNQKQDEKIGLVINTPNPSISLKELHKIYADASSTGIGRSNVYIFWNVVEPVKGEFDWTQSDVLMSYNKNNDLKVTLYFSVINGETLGPFPNWIGKPSLNAIGEDRVVSVLDAILSRYDIIDTVVIAGETESQFRYYEQNIPVYKELFTGVYDKIKEKHPTVKIGNAFALHNVLNKNLEYIVTDLSLGDFVAFSYSPVDTLNEIVKTPQEAKEDLQKIFEIVPDKKIGLFEISWSTSDFVGGNSTSQQEFLEKSFEFYKENKSKIEFFTWYRQYDKPDGTCVIEKPEIGNKTLSVGGGSGLGSSEYVIERLSHYVCSVGLLDADGTPKPSWNEFKNQIELINQ
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+>1001994.MY1_0222
+MWSEKYRPQNISDMIGNEESRSSIIEWFTKWKKGTKPLLLVGPPGIGKTTIAYLTAKQFQYDMVGLNASDVRSKSRINEILSPVLGNVSILGLPMIFIDEVDGIHGRGDYGGAEALIEILKEPTIPIILAANSDTSDKMKSIKKVVKTISFKPIPPRLLKIYLENILKKENVTLSPGSIIKVIDRSRGDVRSMINLTQSLVTGFNPQTEKSFESINVEDGINAFFKANSFDEARGVLYSMQIDPRLKIDAFYSSIVTSNLDNQTLAKLLEIISEADILYGKIMKTQNWRLLRYLNEILIRLYLNDERIRYSQYNLSWPLLNRIRWDGKKIKSLSSVMAKTLHLSSSAFVTICLPYILFCIKNKKLSLDLEETFGDVIEKEIELIK
+>436308.Nmar_0270
+MWSEKYRPQIISDMVGNEESRAAIMEWFAKWKKGTKPLLLAGPPGIGKTTMAFLVAKQFGYDMIGLNASDVRSKSRINEILTPVLGNVSVLGTPMIFVDEVDGIHGRGDYGGVAALVDILKEPTVPIILAANDDTSDKMKNIKKVVKTISFKKIPPRLLRVYLENILKKESAKLSPGSLIKVIDKSRGDIRSMINLTQSMVTGFNPQTETTFENIDVEDGVNAFFKSKSVDEARGVLYSMQIDPREKINAFYSSIVMSSLDPETLAKYLEIISEADMLYGKIVRTQNWRLLRYLNDILIKLYHDDDRVRYAQYNLSWPLLNRIRWDGSKIKSLSSVMAKKLHLSSSAFVTFGLPFVLFCIKNNALELELEETFGDIIEKEIELIQ
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+>1001994.MY1_0691
+MSFKSLIDEIENNLHKILEDMSIYDISFTVEPAKPGFGDASSNISFLLAKSLKKSPKEIANLMSEKYRQSQNILVLKVEPHQTGYLNFFADWEKLNQLILSESNLNEFGFIDLGHNSEIVVEHTSVNPNKALHIGHIRNIVLGDTVARILKKSNYKVNVLNYVDDSGLQVADIIVGFKHLGFAQQSPTGKKFDHYCGDDVYVKTTEKYEQDPNFEEIRKNTLKELEDGASETAKFADTITRRVLENQLETCWNLGVYYDCLNFESQIIRSGLWSKIFEKLKEMNLVEFENDGKNAGCWIIRGENNEEDKVIVRSNGTATYIAKDIPYAAWKLGLIEDPFSYKKYEKTQPGNKILWQTTLTATNEPKQNFTGNKVITVIDSRQARLQKIITGLMSKFKSTNDAYVHLGYESVTLSSDTAQTLGLDTDGKQAQMSGRKGLYVDADSVYDLLKNKTIEETKKRHPEMSDSEIEQIAHYVSVGTLRYEMIKQDLDKMITFDLTKSLSLEGDTAPYIQYTHARASRIIEKSARNPSIDVDFSLLNDASELSLIKIIGLFEIYVLDAAKNLSPKVIARYCHNLAVAFNSFYEHVKVLELGDEKLENSRLCLVNSFKITLEKALELLGITAPEKM
+>436308.Nmar_0686
+MTFKSILDEIENNLNKILDDLSISDVKFSVEPAKPGFGDVSSNVSFLLAKQLKKSPKEISEMLSEKYSQCVSTLVSKSESHPSGYLNFYADWPKLNQLILSESNLPEFGDVDIGKNSTIVVEHTSVNPNKALHIGHIRNIIIGDTISRILQKANYKVNVLNYVDDSGLQVADIIVGFKHFGYPIEPPQGKKFDHYCGDDVYVKTTEKYEQDSSLEEIRKNVLKELEDGTSETAQFADKITRRVLSNQLETCWNLAVSYDCLNFESQIIRSGLWDGIFEKLKEMNLVEFENDGKNAGCWVIRGEGKEEDKVIVRSNGTATYIAKDIPYAAWKLGLLDDPFHYEKYEKEQPNSRVLWQTILNDGASESQNFSGDKVITVIDSRQARLQKIITSLMGKFKSIPDAYVHLGYESVTLSSDTAKILGLETDGKQAQMSGRKGLYVNADSVYDLLKEKTTEETKKRHPEMDDSEIEKISHSVSVATLRYEMIKQDLDKIIAFDLTKSLSLEGDTAPYIQYTHARASRILEKSGRTPSIDVDFSLLKEQSEIDLVKMIGLFNLQVRDAANNLSPKVISRYCHDLAVTFNSFYEKSKVLDLGDEKLENSRLCLVNSFKITIEKALNLLGISAPDKM
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_0879
+MSTEQIEKFQEVVDIPAGVKVTLKKNMMHFEGPLGKTHKNFRNIPVNIEIKEGKVILKSQGYRKRDYSILHTARSVIRNLCEGLVVGYTIKMKIAFAHFPITVKVQDRTVLIENFQGERSSRITKIIGNTKVVPKGEDVILTGEVWNHITQTAANIELRSKVKDKDHRVFLDGVYVYEKKKGIEK
+>436308.Nmar_0794
+MSTSQLEKMQDQVEIPEGVTVTQNKNMLLFEGPLGKTHKNFRNIPVKIEIADGKVNLKTIGERKRDYAILHTARSIIRNICEGLVEGYTIKMKVVFAHFPITVKVEGKKILIENFQGERAPRSTHIMGNTKVIPKGEDVLLTGEVWTDITQTAANIELTTKVKNKDHRVFLDGIYVYEKKKGIEK
+>886738.Nlim_0395
+MSTEQIEKFQEVVEIPKGVTVTLKKHMLHFQGPLGKTHKNFRNIPVNIEVKDGKVILKSQGYRKRDYSILHTARSIIRNICEGLITGYTIKMKIVFAHFPITVKVQDKTVLIENFQGERSARVTRIIGNTKVVPKGEDVILTGEVWNDITQTAANIELRSKVKDKDHRVFLDGVYSYEKKKGIDK
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1727
+MVIEVVRIGQRLVRDDRVTTHVALVARAFGCSKIFMTEVNPEIKDTLEKINNTWGGDFVVEFIDNWKSIVKMKKKDSKIVHLTMYGESINEVDMQLRKEENLLIVVGAEKVPREIYELADYNVGIGNQPHSEISALAIILDRIQKGEQFKNSFPGAKRKIIPTRNGKNVLVRGTRD
+>436308.Nmar_1606
+MVIEVVRIGQRLVRDDRVTTHVALVSRAFGAERIFMTEINPEIKDTLGKINDTWGGNFEIEFIDSWKPIVKKKKEEGFKIVHLSMYGEKINDAQEEIRKEENLLIVVGAEKVPREIYELADFNVGVGSQPHSEISALAILLDRIQGGQQFEKEFPNAKRKIIPTKTGKNVQVKETRD
+>886738.Nlim_1365
+MVLEVVRIGQRLVRDDRVTTHVALVARAFGCTKIFMTEVNPEIKDTVEKINKTWGGDFVVEFIDNWKSIVKKKKEEYKIVHLTMYGESIDDVDEQLRKEKNLLIVVGAEKVPREIYELADYNISIGNQPHSEISALAITLDRIQKGKQFKNSFSGAKRKIIPTKKGKNVFVSGTRD
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1241
+MKIRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISAGEFKAVKMIAAAGLSCEIAGLTRTIKNDIDAAVDAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAVLTKDTVEVTKLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEKKYETNIKSELIYDTSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDAFGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR
+>436308.Nmar_1070
+MTNVRIFDTTLRDGEQTLGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISEGELQAVKMITAAGLSSEICGLTRTIKKDIDAAIDAGLNYVHTFIATSDIHLEHKLQMTREQALEKAIEAVEYGKSHGLQVEFSAEDASRTDREFLKKVFSEVAKAGADRVNIPDTVGYSTPEYMAQITKDTIEATNLPVSVHCHNDFGLAVANALAGIHVGAACAHVTINGIGERAGNASLEELSMALKCLPYEQKYETNIKSELIYDVSRFISKTVGIIVQPNKAIVGANAFGHESGIHTHGVLNNPLTYEPISPELVGRKRWLKVGKHAGVHGMNAMLEEYGVKPTEDQAKQILEKVKVLGDQGKQITDVELLSMASEVLGKKDLKRIVQLTGFSVSTGIGTMPYAFVKLNVDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSGALCEVTVKVEDPLGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVS
+>886738.Nlim_0759
+MKVRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISSGEFKAVKMIASEGLSCEIAGLTRTIKNDVDAAVNAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAELTRDTVEATHLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEQKYETNIKSELIYETSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDALGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1343
+MQNQKSEWATNESPRIMSYTLANFRQLPQIQKLGEEKQFEMEVVGNVLPFKTNNYVVEQLIDWNNIPDDPMFVLTFPQRGMLIPEHYAKMEAALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMKEGEQLVQYLQEHPEISDVLFTGGDPMIMKARIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTDDDAEEMLDIFKRVVDKGIHLALMGHFNHTVELKTDAVKEAIKKVRATGAQIRTQSPILRHINDDSEMWAEMWKTQVQLGCIPYYMFVVRDTGAQHYFGIPLIEAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGIAEYGGEKLMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFEDELNEKMKVIKNQDYPES
+>436308.Nmar_1772
+MTYQESVWDDSPSLKSYTLSNFRDLPQIQNISEEKQFEMEVVGNVLPFKANNYVVEQLINWNDIPNDPMYVLTFPQRGMLKPEHYAKMENTLKNTSDKKEIANVANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDEMKFAMQEGEQLVQYVSEHPEISDVLFTGGDPMIMKAKMFSKYVDALIEAKLPNLKTIRIGTKALSYWPYKFLTDSDSQEMLQVFQKITDSGLHLAFMAHFNHLNELSTNAVKSAIKEVRKTGAQIRTQSPLLAHINDDAEMWANMWTKQVQLGCIPYYMFVVRDTGAQHYFGVPLVKAYEIFSQAYSTVSGLGRTVRGPSMSATPGKVQVVGTTQINGEKLLILRFLQGRNPNWIKEPFFAKYDENAIWLDDLKPAFGDKFFFEDELDAIKASKTS
+>886738.Nlim_0892
+MQRQDSAWGVKESPRLKSYTLANFRELPQIQKMGAKKQFEMEVVGNVLPFKTNNYVIEQLIDWNNIPNDPMFVLTFPQRGMLIPEHYSKMESALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMREGEQLVQYLREHPEISDVLFTGGDPMIMKAKIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTEDDAEEMLDIFKRVVDKGIHLAVMGHFNHLVELKTDAVKEAIKKIRATGAQIRTQSPLLRHINDDADMWAEMWKVQVQLGCIPYYMFVVRDTGAQHYFGISLIDAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGITEVNDEKFMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFENELKEMMMTIKNEDYPES
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1050
+MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLEKIKQNNYDAVIISPGPGTPTDRKYFGICSDVIKDMGSTTPILGVCLGHQGIIHAFGGKVTNAGCVRHGKTSPVDHTNSDLFKDVKNPFRATRYHSLVGDKTIIPDVLEVTAVAADDGEVMAVRHKEYLIEGVQFHPESIMTEDGKKILANFIKQVKDRK
+>436308.Nmar_0912
+MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLNEIQEKKYDAIIISPGPGTPEDKKYFGVCSEVIKDMGSSTPILGVCLGHQGIIDAFGGKVTNAGCVRHGKTSPVNHEDSKLFKDVKNPFRATRYHSLVGDKTIIPEVLKVTATASDDGEVMAIEHKDYLIQGVQFHPESIMTEDGKKILSNFIQQVKEKQK
+>886738.Nlim_0576
+MKFLIIDNYDSFVYNIAQYLGELGVDSDVIRNDKITVEQIKQNKYDAIIISPGPGTPSDRKYFGVCGDVIKDIGPITPILGVCLGHQGIIEAFGGKVTNARCVRHGKTSPVDHTNSELFKDVKNPFRATRYHSLVGDKTIIPDALEITAIAADDGEVMAVRHKKYLIEGVQFHPESIMTEDGKKILANFIKQVKSKK
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1793
+MMGDRDYRSIIKNAVDSIGRELEIEIDAKDIKTIHLKEVVQCLRRSYYDRIEPKEVERRGFNDLLSGLLRKLQYGSDPKEFSIEDIKLRGHADMIADNSIILFRPTNASLESPLANDLLYLNACMWIYDKTDGVIIYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSSDCMECQYYQRCFITKKNTKQVSLAEMLGLGKD
+>436308.Nmar_1701
+MMGDRDFRTTIQNAIKSIGNELEIDIDSKDFETIHLQEVVRCMRRSYYDRVEPLEIERRGFNELLSGLLRKLEYGSNPKDFDINEIKLRGQADMMVDDAILLFRSATEELENPHASDVLYLNACMWIYDKEDGMIVYITGDRKESTFSLTRNKKMFEDTIRRVRVLNNLLKEQKTPILEPSAECTECQYYERCFTKRKNTKQTSLAEMLGLGKQD
+>886738.Nlim_1425
+MMGDRDFRSIVKNAVDTIGRELEIQIDAKNIKTIHLKEVVQCLRRSYYDRIDPKEVERRGFNDLLSGLLRKLHYGSDPKEFSIDEIKLRGQADMIADDSIVLFRPSKTVIEAPVANDLLYLNACMWIYDKTDGIIVYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSNDCAECQYYQRCFTTKKNTKQVSLAEMIGLGKD
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,6 @@
+>1001994.MY1_1440
+MAEKGILAFSGGLDTSVVIKYLQEEYNMDVITVTVDVGQGDDQKKIEAKAKKLGVIKHYNIDARKEFVENFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELEFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYNEPPEDAFIWVKTKNLPDKPTYLEIKFEKGIPVSVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDAFIQASQKPVSGTVKLKLFKGSIRVVGRKSDYSLYNHKIATYGTESTFDQRLAKGFVELWGIQSTEANKLQKKRSTKT
+>436308.Nmar_1286
+MTQKGILAFSGGLDTSVVVKYLQDEHDMDVITVTVDVGQGDDNKKIAAKAKKLGVKKHYNIDARKEFVKDYIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSNLPIIAPIRDKNLDRVTELKFAKKHGIEIDTVAKKFSIDQNLWGRAIEGGVLEDPYNEPPDDAFIWVKTKNLPDKPTYLEIKFEKGIPVGVDGKTMDGQKLIEYINKKAGDAGVGIVDHIEDRVVGIKSREVYETPAATCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKSDLDGFIEASQKPVTGTVKLKLYKGSLRVVGRKSKNSLYSHEIATYGTESTFDQRLAKGFVELWGMQSTEANKLQKKRSTKI
+>886738.Nlim_1021
+MTEKGILAFSGGLDTSVVVKYLQEEYDMDVITVTVDVGQGDDQRKIEAKAKKLGVKKHYNIDARKEFVEKFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELAFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYSEPPDDAFIWVKTKNLPDKPTYIEIKFEKGIPVAVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDSFIETSQKPVTGTVKIKLFKGSMRVVGRKSDYSLYSHKIATYGSESTFDQKMAKGFVELWGIQSTEANKLQKKRSTKI
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/eggnog.db
Binary file test-data/cached_locally/eggnog.db has changed
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/eggnog_mapper.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_mapper.loc	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,4 @@
+#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 000000000000 -r f4e5279b5d10 test-data/cached_locally/eggnog_proteins.dmnd
Binary file test-data/cached_locally/eggnog_proteins.dmnd has changed
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,637 @@
+HMMER3/f [3.1b1 | May 2013]
+NAME  ENOG411CB2I
+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 - - -
+          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
+     11   2.67125  4.89170  2.63995  2.01286  4.19991  3.30620  3.62584  3.60098  2.37369  3.19109  4.03621  2.84971  3.79086  2.33541  2.77812  2.67728  2.37271  3.26758  5.41474  4.07676     12 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
+     12   3.08388  4.45892  4.50779  3.99931  3.20318  4.29602  4.67441  1.39467  3.81924  1.46323  3.07061  4.27722  4.58606  4.09884  4.01845  3.66823  3.33503  1.84767  5.18001  3.96570     13 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
+     13   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     14 y - - -
+          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
+     14   2.98251  4.43779  4.31388  3.82115  3.20877  4.08952  4.54007  2.00695  3.64555  1.30599  3.09552  4.09798  4.45211  3.94746  3.86362  3.46665  3.25564  1.64211  5.13725  3.91385     15 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
+     15   2.15254  2.45969  3.69479  3.31339  3.86059  2.92557  4.16344  3.17236  3.21287  2.97886  3.87676  3.36254  3.65358  3.52003  3.46091  1.53946  2.62341  2.77195  5.29578  4.07476     16 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
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    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 - - -
+          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
+    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 - - -
+          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
+    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 - - -
+          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
+    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 - - -
+          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
+    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 - - -
+          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
+          0.02203  3.82629        *  0.61958  0.77255  0.00000        *
+//
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3f
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diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3i
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3i has changed
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3m
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3m has changed
diff -r 000000000000 -r f4e5279b5d10 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3p
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3p has changed
diff -r 000000000000 -r f4e5279b5d10 test-data/make_comp_file.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_comp_file.sh	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+base_path=$1
+
+emapper.py \
+    -i $base_path/test-data/nlim_fragment.fasta \
+    --output HMM_nlim \
+    --output_dir $base_path/test-data \
+    --override \
+    --database $base_path/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I \
+    --data_dir $base_path/test-data/cached_locally \
+    --no_refine\
+    --no_annot \
+    --no_file_comments
+
+emapper.py \
+    -i $base_path/test-data/nlim_fragment.fasta \
+    --output DIA_nlim \
+    --output_dir $base_path/test-data \
+    --override \
+    -m diamond \
+    --data_dir $base_path/test-data/cached_locally \
+    --no_file_comments \
+    --no_annot
diff -r 000000000000 -r f4e5279b5d10 test-data/nlim_1033.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nlim_1033.fasta	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,7 @@
+>Nlim_1033886738.Nlim_1033Cytidyltransferase-like protein 
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLE
+IDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHP
+GHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKE
+QRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGY
+DQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQK
+EYGESIHGI
diff -r 000000000000 -r f4e5279b5d10 test-data/nlim_fragment.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nlim_fragment.fasta	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,2 @@
+>Nlim_1033886738.Nlim_1033Cytidyltransferase-like protein 
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLE
diff -r 000000000000 -r f4e5279b5d10 tool-data/eggnog_mapper.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper.loc.sample	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,30 @@
+#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 000000000000 -r f4e5279b5d10 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,7 @@
+<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>
+</tables>
diff -r 000000000000 -r f4e5279b5d10 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Oct 31 14:17:50 2017 -0400
@@ -0,0 +1,7 @@
+<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>
+</tables>