Mercurial > repos > galaxyp > eggnog_mapper
diff eggnog_mapper.xml @ 0:f4e5279b5d10 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
| author | galaxyp |
|---|---|
| date | Tue, 31 Oct 2017 14:17:50 -0400 |
| parents | |
| children | 3c7c9396daaa |
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--- /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>