--- /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>