Mercurial > repos > jjohnson > eggnog_mapper
diff eggnog_mapper.xml @ 0:b3ae16ffb54e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
| author | jjohnson |
|---|---|
| date | Fri, 26 May 2017 11:45:10 -0400 |
| parents | |
| children | 7de7487a7e8d |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eggnog_mapper.xml Fri May 26 11:45:10 2017 -0400 @@ -0,0 +1,364 @@ +<tool id="eggnog_mapper" name="eggNOG Mapper" version="0.1.0"> + <description>functional sequence annotation by orthology</description> + <requirements> + <requirement type="package" version="0.99.2">eggnog-mapper</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <version_command>python emapper.py --version</version_command> + <command><![CDATA[ + ### Load on demand - with changes to download_eggnog_data.py + ## #if $db.mode == 'hmmer': + ## download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database && + ## #else + ## download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database && + ## #end if + emapper.py + --data_dir '$eggnog_data.fields.data_dir' + -m $db.mode $translate + #if $db.mode == 'hmmer': + --database=$db.database + #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 + #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 $seed_ortholog_options.seed_ortholog_score: + --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score + #end if + $output_options.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="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" + label="Are these CDS sequences that need to be translated"/> + <param name="eggnog_data" type="select" label="Eggnog Data"> + <options from_data_table="eggnog_mapper" > + <filter type="static_value" name="type" value="data" column="2"/> + <validator type="no_options" message="No cached eggnog data is available" /> + </options> + </param> + <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" multiple="true" min="1" label="HMM target database"> + <options from_data_table="eggnog_mapper" > + <filter type="param_value" ref="eggnog_data" key="data_dir" column="3" /> + <filter type="static_value" name="type" value="hmm" column="2"/> + <validator type="no_options" message="No HMM DBs are available, request 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. Default=1" /> + <param name="hmm_evalue" type="float" value="0.001" label="E-value threshold. Default=0.001" /> + <param name="hmm_score" type="integer" value="20" label="Bit score threshold. Default=20" /> + <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="" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" /> + </when> + </conditional> + </when> + <when value="diamond"> + <param name="database" type="hidden" value="diamond"/> + </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" optional="true" 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">all</option> + </param> + <param name="go_evidence" type="select" optional="true" label="Type of GO terms should be used for annotation"> + <option value="experimental">experimental = Use only terms inferred from experimental evidence</option> + <option value="non-electronic">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" optional="true" label="Min E-value threshold. Default=0.001"> + <help> + Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. + Queries not having a significant seed orthologs will not be annotated. + </help> + </param> + <param name="seed_ortholog_score" type="integer" value="60" optional="true" label="Bit score threshold. Default=60"> + <help> + Min bit score expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. + Queries not having a significant seed orthologs will not be annotated. Default=60 + </help> + </param> + </section> + <section name="output_options" expanded="false" title="Output Options"> + <param name="file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="false" + 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}: ${db.database}.annotations" from_work_dir="results.emapper.annotations"> + <filter>output_options['no_annot'] == ''</filter> + <actions> + <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/> + </actions> + </data> + <data name="hmm_hits" format="tabular" label="${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> + <help><![CDATA[ + +eggnog-mapper + +optional arguments: + -h, --help show this help message and exit + --version + +Target HMM Database Options: + --guessdb guess eggnog db based on the provided taxid + --database , -d specify the target database for sequence searches. + Choose among: euk,bact,arch, host:port, or a local + hmmpressed database + --dbtype {hmmdb,seqdb} + --qtype {hmm,seq} + +Annotation Options: + --tax_scope Fix the taxonomic scope used for annotation, so only + orthologs from a particular clade are used for + functional transfer. By default, this is automatically + adjusted for every query sequence. + --target_orthologs {one2one,many2one,one2many,many2many,all} + defines what type of orthologs should be used for + functional transfer + --excluded_taxa (for debugging and benchmark purposes) + --go_evidence {experimental,non-electronic} + Defines what type of GO terms should be used for + annotation:experimental = Use only terms inferred from + experimental evidencenon-electronic = Use only non- + electronically curated terms + +HMM search_options: + --hmm_maxhits Max number of hits to report. Default=1 + --hmm_evalue E-value threshold. Default=0.001 + --hmm_score Bit score threshold. Default=20 + --hmm_maxseqlen Ignore query sequences larger than `maxseqlen`. + Default=5000 + --hmm_qcov min query coverage (from 0 to 1). Default=(disabled) + --Z Fixed database size used in phmmer/hmmscan (allows + comparing e-values among databases). + Default=40,000,000 + +Seed ortholog search option: + --seed_ortholog_evalue + Min E-value expected when searching for seed eggNOG + ortholog. Applies to phmmer/diamond searches. Queries + not having a significant seed orthologs will not be + annotated. Default=0.001 + --seed_ortholog_score + Min bit score expected when searching for seed eggNOG + ortholog. Applies to phmmer/diamond searches. Queries + not having a significant seed orthologs will not be + annotated. Default=60 + +Output options: + --output , -o base name for output files + --resume Resumes a previous execution skipping reported hits in + the output file. + --override Overwrites output files if they exist. + --no_refine Skip hit refinement, reporting only HMM hits. + --no_annot Skip functional annotation, reporting only hits + --no_search Skip HMM search mapping. Use existing hits file + --report_orthologs The list of orthologs used for functional transferred + are dumped into a separate file + --scratch_dir Write output files in a temporary scratch dir, move + them to final the final output dir when finished. + Speed up large computations using network file + systems. + --output_dir Where output files should be written + --temp_dir Where temporary files are created. Better if this is a + local disk. + --no_file_comments No header lines nor stats are included in the output + files + --keep_mapping_files Do not delete temporary mapping files used for + annotation (i.e. HMMER and DIAMOND search outputs) + +Execution options: + -m {hmmer,diamond} Default:hmmer + -i Computes annotations for the provided FASTA file + --translate Assume sequences are genes instead of proteins + --servermode Loads target database in memory and keeps running in + server mode, so another instance of eggnog-mapper can + connect to this sever. Auto turns on the --usemem flag + --usemem If a local hmmpressed database is provided as target + using --db, this flag will allocate the whole database + in memory using hmmpgmd. Database will be unloaded + after execution. + --cpu + --annotate_hits_table + Annotatate TSV formatted table of query->hits. 4 + fields required: query, hit, evalue, score. Implies + --no_search and --no_refine. + + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gkv1248</citation> + </citations> +</tool>