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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
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="0.1.0">
2 <description>functional sequence annotation by orthology</description>
3 <requirements>
4 <requirement type="package" version="0.99.2">eggnog-mapper</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <version_command>python emapper.py --version</version_command>
10 <command><![CDATA[
11 ### Load on demand - with changes to download_eggnog_data.py
12 ## #if $db.mode == 'hmmer':
13 ## download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database &&
14 ## #else
15 ## download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database &&
16 ## #end if
17 emapper.py
18 --data_dir '$eggnog_data.fields.data_dir'
19 -m $db.mode $translate
20 #if $db.mode == 'hmmer':
21 --database=$db.database
22 #if $db.hmm_options.hmm_settings == 'specified':
23 --hmm_maxhits=$db.hmm_options.hmm_maxhits
24 --hmm_evalue=$db.hmm_options.hmm_evalue
25 --hmm_score=$db.hmm_options.hmm_score
26 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
27 #if str($db.hmm_options.hmm_qcov):
28 --hmm_qcov=$db.hmm_options.hmm_qcov
29 #end if
30 --Z=$db.hmm_options.Z
31 #end if
32 #end if
33 #if $annotation_options.tax_scope:
34 --tax_scope=$annotation_options.tax_scope
35 #end if
36 #if $annotation_options.target_orthologs:
37 --target_orthologs=$annotation_options.target_orthologs
38 #end if
39 #if $annotation_options.go_evidence:
40 --go_evidence=$annotation_options.go_evidence
41 #end if
42 #if $seed_ortholog_options.seed_ortholog_evalue:
43 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
44 #end if
45 #if $seed_ortholog_options.seed_ortholog_score:
46 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
47 #end if
48 $output_options.file_comments
49 $output_options.no_annot
50 $output_options.report_orthologs
51 --output='results'
52 -i '${input}'
53 ]]></command>
54 <inputs>
55 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
56 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
57 label="Are these CDS sequences that need to be translated"/>
58 <param name="eggnog_data" type="select" label="Eggnog Data">
59 <options from_data_table="eggnog_mapper" >
60 <filter type="static_value" name="type" value="data" column="2"/>
61 <validator type="no_options" message="No cached eggnog data is available" />
62 </options>
63 </param>
64 <conditional name="db">
65 <param name="mode" type="select" label="Annotation Type">
66 <option value="hmmer">HMM</option>
67 <option value="diamond">DIAMOND</option>
68 </param>
69 <when value="hmmer">
70 <param name="database" type="select" multiple="true" min="1" label="HMM target database">
71 <options from_data_table="eggnog_mapper" >
72 <filter type="param_value" ref="eggnog_data" key="data_dir" column="3" />
73 <filter type="static_value" name="type" value="hmm" column="2"/>
74 <validator type="no_options" message="No HMM DBs are available, request from your galaxy admin" />
75 </options>
76 </param>
77 <conditional name="hmm_options">
78 <param name="hmm_settings" type="select" label="HMM Search Options">
79 <option value="default">Use defaults</option>
80 <option value="specified">Set HMM Search Options</option>
81 </param>
82 <when value="default"/>
83 <when value="specified">
84 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report. Default=1" />
85 <param name="hmm_evalue" type="float" value="0.001" label="E-value threshold. Default=0.001" />
86 <param name="hmm_score" type="integer" value="20" label="Bit score threshold. Default=20" />
87 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" />
88 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
89 <param name="Z" type="integer" value="" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" />
90 </when>
91 </conditional>
92 </when>
93 <when value="diamond">
94 <param name="database" type="hidden" value="diamond"/>
95 </when>
96 </conditional>
97 <section name="annotation_options" expanded="false" title="Annotation Options">
98 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
99 <option value="NOG">All organisms (NOG)</option>
100 <option value="aciNOG">Acidobacteria (aciNOG)</option>
101 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
102 <option value="acoNOG">Aconoidasida (acoNOG)</option>
103 <option value="actNOG">Actinobacteria (actNOG)</option>
104 <option value="agaNOG">Agaricales (agaNOG)</option>
105 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
106 <option value="apiNOG">Apicomplexa (apiNOG)</option>
107 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
108 <option value="aquNOG">Aquificae (aquNOG)</option>
109 <option value="arNOG">Archaea (arNOG)</option>
110 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
111 <option value="artNOG">Arthropoda (artNOG)</option>
112 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
113 <option value="ascNOG">Ascomycota (ascNOG)</option>
114 <option value="aveNOG">Aves (aveNOG)</option>
115 <option value="bacNOG">Bacilli (bacNOG)</option>
116 <option value="bactNOG">Bacteria (bactNOG)</option>
117 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
118 <option value="basNOG">Basidiomycota (basNOG)</option>
119 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
120 <option value="biNOG">Bilateria (biNOG)</option>
121 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
122 <option value="braNOG">Brassicales (braNOG)</option>
123 <option value="carNOG">Carnivora (carNOG)</option>
124 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
125 <option value="chlNOG">Chlorobi (chlNOG)</option>
126 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
127 <option value="chloNOG">Chloroflexi (chloNOG)</option>
128 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
129 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
130 <option value="chorNOG">Chordata (chorNOG)</option>
131 <option value="chrNOG">Chromadorea (chrNOG)</option>
132 <option value="cloNOG">Clostridia (cloNOG)</option>
133 <option value="cocNOG">Coccidia (cocNOG)</option>
134 <option value="creNOG">Crenarchaeota (creNOG)</option>
135 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
136 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
137 <option value="cytNOG">Cytophagia (cytNOG)</option>
138 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
139 <option value="defNOG">Deferribacteres (defNOG)</option>
140 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
141 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
142 <option value="delNOG">delta/epsilon (delNOG)</option>
143 <option value="dipNOG">Diptera (dipNOG)</option>
144 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
145 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
146 <option value="droNOG">Drosophilidae (droNOG)</option>
147 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
148 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
149 <option value="euNOG">Eukaryotes (euNOG)</option>
150 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
151 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
152 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
153 <option value="fiNOG">Fishes (fiNOG)</option>
154 <option value="firmNOG">Firmicutes (firmNOG)</option>
155 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
156 <option value="fuNOG">Fungi (fuNOG)</option>
157 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
158 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
159 <option value="haeNOG">Haemosporida (haeNOG)</option>
160 <option value="halNOG">Halobacteria (halNOG)</option>
161 <option value="homNOG">Hominidae (homNOG)</option>
162 <option value="hymNOG">Hymenoptera (hymNOG)</option>
163 <option value="hypNOG">Hypocreales (hypNOG)</option>
164 <option value="inNOG">Insects (inNOG)</option>
165 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
166 <option value="lepNOG">Lepidoptera (lepNOG)</option>
167 <option value="lilNOG">Liliopsida (lilNOG)</option>
168 <option value="maNOG">Mammals (maNOG)</option>
169 <option value="magNOG">Magnaporthales (magNOG)</option>
170 <option value="meNOG">Animals (meNOG)</option>
171 <option value="metNOG">Methanobacteria (metNOG)</option>
172 <option value="methNOG">Methanococci (methNOG)</option>
173 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
174 <option value="necNOG">Nectriaceae (necNOG)</option>
175 <option value="negNOG">Negativicutes (negNOG)</option>
176 <option value="nemNOG">Nematodes (nemNOG)</option>
177 <option value="onyNOG">Onygenales (onyNOG)</option>
178 <option value="opiNOG">Opisthokonts (opiNOG)</option>
179 <option value="perNOG">Peronosporales (perNOG)</option>
180 <option value="plaNOG">Planctomycetes (plaNOG)</option>
181 <option value="pleNOG">Pleosporales (pleNOG)</option>
182 <option value="poaNOG">Poales (poaNOG)</option>
183 <option value="prNOG">Primates (prNOG)</option>
184 <option value="proNOG">Proteobacteria (proNOG)</option>
185 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
186 <option value="roNOG">Rodents (roNOG)</option>
187 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
188 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
189 <option value="sorNOG">Sordariales (sorNOG)</option>
190 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
191 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
192 <option value="spiNOG">Spirochaetes (spiNOG)</option>
193 <option value="spriNOG">Supraprimates (spriNOG)</option>
194 <option value="strNOG">Streptophyta (strNOG)</option>
195 <option value="synNOG">Synergistetes (synNOG)</option>
196 <option value="tenNOG">Tenericutes (tenNOG)</option>
197 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
198 <option value="theNOG">Thermoplasmata (theNOG)</option>
199 <option value="therNOG">Thermotogae (therNOG)</option>
200 <option value="thermNOG">Thermococci (thermNOG)</option>
201 <option value="treNOG">Tremellales (treNOG)</option>
202 <option value="veNOG">Vertebrates (veNOG)</option>
203 <option value="verNOG">Verrucomicrobia (verNOG)</option>
204 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
205 <option value="virNOG">Viridiplantae (virNOG)</option>
206 </param>
207 <param name="target_orthologs" type="select" optional="true" label="target orthologs for functional transfer">
208 <option value="one2one">one2one</option>
209 <option value="many2one">many2one</option>
210 <option value="one2many">one2many</option>
211 <option value="many2many">many2many</option>
212 <option value="all">all</option>
213 </param>
214 <param name="go_evidence" type="select" optional="true" label="Type of GO terms should be used for annotation">
215 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
216 <option value="non-electronic">non-electronic = Use only non-electronically curated terms</option>
217 </param>
218 </section>
219 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
220 <param name="seed_ortholog_evalue" type="float" value="0.001" optional="true" label="Min E-value threshold. Default=0.001">
221 <help>
222 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
223 Queries not having a significant seed orthologs will not be annotated.
224 </help>
225 </param>
226 <param name="seed_ortholog_score" type="integer" value="60" optional="true" label="Bit score threshold. Default=60">
227 <help>
228 Min bit score expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
229 Queries not having a significant seed orthologs will not be annotated. Default=60
230 </help>
231 </param>
232 </section>
233 <section name="output_options" expanded="false" title="Output Options">
234 <param name="file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="false"
235 label="Exclude header lines and stats from output files"/>
236 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
237 label="Skip functional annotation, reporting only hits"/>
238 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
239 label="Output a file with the list of orthologs for each hits"/>
240 </section>
241 </inputs>
242 <outputs>
243 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
244 <actions>
245 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
246 </actions>
247 </data>
248 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
249 <filter>output_options['no_annot'] == ''</filter>
250 <actions>
251 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>
252 </actions>
253 </data>
254 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits">
255 <filter>db['mode'] == 'hmmer'</filter>
256 <actions>
257 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
258 </actions>
259 </data>
260 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
261 <filter>output_options['report_orthologs']</filter>
262 <actions>
263 <action name="column_names" type="metadata" default="query_name,orthologs"/>
264 </actions>
265 </data>
266 </outputs>
267 <help><![CDATA[
268
269 eggnog-mapper
270
271 optional arguments:
272 -h, --help show this help message and exit
273 --version
274
275 Target HMM Database Options:
276 --guessdb guess eggnog db based on the provided taxid
277 --database , -d specify the target database for sequence searches.
278 Choose among: euk,bact,arch, host:port, or a local
279 hmmpressed database
280 --dbtype {hmmdb,seqdb}
281 --qtype {hmm,seq}
282
283 Annotation Options:
284 --tax_scope Fix the taxonomic scope used for annotation, so only
285 orthologs from a particular clade are used for
286 functional transfer. By default, this is automatically
287 adjusted for every query sequence.
288 --target_orthologs {one2one,many2one,one2many,many2many,all}
289 defines what type of orthologs should be used for
290 functional transfer
291 --excluded_taxa (for debugging and benchmark purposes)
292 --go_evidence {experimental,non-electronic}
293 Defines what type of GO terms should be used for
294 annotation:experimental = Use only terms inferred from
295 experimental evidencenon-electronic = Use only non-
296 electronically curated terms
297
298 HMM search_options:
299 --hmm_maxhits Max number of hits to report. Default=1
300 --hmm_evalue E-value threshold. Default=0.001
301 --hmm_score Bit score threshold. Default=20
302 --hmm_maxseqlen Ignore query sequences larger than `maxseqlen`.
303 Default=5000
304 --hmm_qcov min query coverage (from 0 to 1). Default=(disabled)
305 --Z Fixed database size used in phmmer/hmmscan (allows
306 comparing e-values among databases).
307 Default=40,000,000
308
309 Seed ortholog search option:
310 --seed_ortholog_evalue
311 Min E-value expected when searching for seed eggNOG
312 ortholog. Applies to phmmer/diamond searches. Queries
313 not having a significant seed orthologs will not be
314 annotated. Default=0.001
315 --seed_ortholog_score
316 Min bit score expected when searching for seed eggNOG
317 ortholog. Applies to phmmer/diamond searches. Queries
318 not having a significant seed orthologs will not be
319 annotated. Default=60
320
321 Output options:
322 --output , -o base name for output files
323 --resume Resumes a previous execution skipping reported hits in
324 the output file.
325 --override Overwrites output files if they exist.
326 --no_refine Skip hit refinement, reporting only HMM hits.
327 --no_annot Skip functional annotation, reporting only hits
328 --no_search Skip HMM search mapping. Use existing hits file
329 --report_orthologs The list of orthologs used for functional transferred
330 are dumped into a separate file
331 --scratch_dir Write output files in a temporary scratch dir, move
332 them to final the final output dir when finished.
333 Speed up large computations using network file
334 systems.
335 --output_dir Where output files should be written
336 --temp_dir Where temporary files are created. Better if this is a
337 local disk.
338 --no_file_comments No header lines nor stats are included in the output
339 files
340 --keep_mapping_files Do not delete temporary mapping files used for
341 annotation (i.e. HMMER and DIAMOND search outputs)
342
343 Execution options:
344 -m {hmmer,diamond} Default:hmmer
345 -i Computes annotations for the provided FASTA file
346 --translate Assume sequences are genes instead of proteins
347 --servermode Loads target database in memory and keeps running in
348 server mode, so another instance of eggnog-mapper can
349 connect to this sever. Auto turns on the --usemem flag
350 --usemem If a local hmmpressed database is provided as target
351 using --db, this flag will allocate the whole database
352 in memory using hmmpgmd. Database will be unloaded
353 after execution.
354 --cpu
355 --annotate_hits_table
356 Annotatate TSV formatted table of query->hits. 4
357 fields required: query, hit, evalue, score. Implies
358 --no_search and --no_refine.
359
360 ]]></help>
361 <citations>
362 <citation type="doi">10.1093/nar/gkv1248</citation>
363 </citations>
364 </tool>