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comparison eggnog_mapper.xml @ 0:2354d9b43a91 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
author galaxyp
date Tue, 31 Oct 2017 14:17:30 -0400
parents
children ca04bdc749da
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-1:000000000000 0:2354d9b43a91
1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="1.0.1">
2 <description>functional sequence annotation by orthology</description>
3 <requirements>
4 <requirement type="package" version="1.0.1">eggnog-mapper</requirement>
5 </requirements>
6 <version_command>emapper.py --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[
8 emapper.py
9 --data_dir '$eggnog_data.fields.db'
10 -m $db.mode
11 $translate
12 #if ($db.mode == 'hmmer'):
13 --database=$db.database.fields.db
14 #if $db.hmm_options.hmm_settings == 'specified':
15 --hmm_maxhits=$db.hmm_options.hmm_maxhits
16 --hmm_evalue=$db.hmm_options.hmm_evalue
17 --hmm_score=$db.hmm_options.hmm_score
18 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
19 #if str($db.hmm_options.hmm_qcov):
20 --hmm_qcov=$db.hmm_options.hmm_qcov
21 #end if
22 --Z=$db.hmm_options.Z
23 #end if
24 #elif ($db.mode == 'diamond'):
25 --matrix '$db.matrix_gapcosts.matrix'
26 $db.matrix_gapcosts.gap_costs
27 #end if
28 #if $annotation_options.tax_scope:
29 --tax_scope=$annotation_options.tax_scope
30 #end if
31 #if $annotation_options.target_orthologs:
32 --target_orthologs=$annotation_options.target_orthologs
33 #end if
34 #if $annotation_options.go_evidence:
35 --go_evidence=$annotation_options.go_evidence
36 #end if
37 #if $seed_ortholog_options.seed_ortholog_evalue:
38 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
39 #end if
40 #if str($seed_ortholog_options.seed_ortholog_score):
41 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
42 #end if
43 $output_options.no_file_comments
44 $output_options.no_annot
45 $output_options.report_orthologs
46 --output='results'
47 -i '${input}'
48 ]]></command>
49 <inputs>
50 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
51 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
52 <options from_data_table="eggnog_mapper">
53 <filter type="static_value" name="type" value="data" column="2"/>
54 </options>
55 </param>
56 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
57 label="Are these coding DNA sequences that need to be translated?"/>
58 <conditional name="db">
59 <param name="mode" type="select" label="Annotation Type">
60 <option value="hmmer">HMM</option>
61 <option value="diamond">DIAMOND</option>
62 </param>
63 <when value="hmmer">
64 <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.">
65 <options from_data_table="eggnog_mapper">
66 <filter type="static_value" value="hmmer" column="2"/>
67 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
68 </options>
69 </param>
70 <conditional name="hmm_options">
71 <param name="hmm_settings" type="select" label="HMM Search Options">
72 <option value="default">Use defaults</option>
73 <option value="specified">Set HMM Search Options</option>
74 </param>
75 <when value="default"/>
76 <when value="specified">
77 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
78 <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" />
79 <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
80 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" />
81 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
82 <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" />
83 </when>
84 </conditional>
85 </when>
86 <when value="diamond">
87 <!-- db.database is used in diamond mode only to name outputs -->
88 <param name="database" type="hidden" value="diamond"/>
89 <conditional name="matrix_gapcosts">
90 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
91 <option value="BLOSUM90">BLOSUM90</option>
92 <option value="BLOSUM80">BLOSUM80</option>
93 <option value="BLOSUM62" selected="true">BLOSUM62</option>
94 <option value="BLOSUM50">BLOSUM50</option>
95 <option value="BLOSUM45">BLOSUM45</option>
96 <option value="PAM250">PAM250</option>
97 <option value="PAM70">PAM70</option>
98 <option value="PAM30">PAM30</option>
99 </param>
100 <when value="BLOSUM90">
101 <param name="gap_costs" type="select" label="Gap Costs">
102 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
103 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
104 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
105 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
106 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
107 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
108 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
109 </param>
110 </when>
111 <when value="BLOSUM80">
112 <param name="gap_costs" type="select" label="Gap Costs">
113 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
114 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
115 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
116 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
117 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
118 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
119 </param>
120 </when>
121 <when value="BLOSUM62">
122 <param name="gap_costs" type="select" label="Gap Costs">
123 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
124 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
125 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
126 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
127 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
128 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
129 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
130 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
131 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
132 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
134 </param>
135 </when>
136 <when value="BLOSUM50">
137 <param name="gap_costs" type="select" label="Gap Costs">
138 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
139 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
140 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
141 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
142 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
143 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
144 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
145 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
146 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
147 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
148 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
149 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
150 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
151 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
152 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
153 </param>
154 </when>
155 <when value="BLOSUM45">
156 <param name="gap_costs" type="select" label="Gap Costs">
157 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
158 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
159 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
160 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
161 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
162 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
163 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
164 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
165 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
166 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
167 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
168 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
169 </param>
170 </when>
171 <when value="PAM250">
172 <param name="gap_costs" type="select" label="Gap Costs">
173 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
174 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
175 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
176 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
177 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
178 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
179 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
180 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
181 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
182 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
183 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
184 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
185 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
186 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
187 </param>
188 </when>
189 <when value="PAM70">
190 <param name="gap_costs" type="select" label="Gap Costs">
191 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
192 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
193 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
194 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
195 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
196 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
197 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
198 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
199 </param>
200 </when>
201 <when value="PAM30">
202 <param name="gap_costs" type="select" label="Gap Costs">
203 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
204 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
205 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
206 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
207 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
208 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
209 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
210 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
211 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
212 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
213 </param>
214 </when>
215 </conditional>
216 </when>
217 </conditional>
218 <section name="annotation_options" expanded="false" title="Annotation Options">
219 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
220 <option value="NOG">All organisms (NOG)</option>
221 <option value="aciNOG">Acidobacteria (aciNOG)</option>
222 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
223 <option value="acoNOG">Aconoidasida (acoNOG)</option>
224 <option value="actNOG">Actinobacteria (actNOG)</option>
225 <option value="agaNOG">Agaricales (agaNOG)</option>
226 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
227 <option value="apiNOG">Apicomplexa (apiNOG)</option>
228 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
229 <option value="aquNOG">Aquificae (aquNOG)</option>
230 <option value="arNOG">Archaea (arNOG)</option>
231 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
232 <option value="artNOG">Arthropoda (artNOG)</option>
233 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
234 <option value="ascNOG">Ascomycota (ascNOG)</option>
235 <option value="aveNOG">Aves (aveNOG)</option>
236 <option value="bacNOG">Bacilli (bacNOG)</option>
237 <option value="bactNOG">Bacteria (bactNOG)</option>
238 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
239 <option value="basNOG">Basidiomycota (basNOG)</option>
240 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
241 <option value="biNOG">Bilateria (biNOG)</option>
242 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
243 <option value="braNOG">Brassicales (braNOG)</option>
244 <option value="carNOG">Carnivora (carNOG)</option>
245 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
246 <option value="chlNOG">Chlorobi (chlNOG)</option>
247 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
248 <option value="chloNOG">Chloroflexi (chloNOG)</option>
249 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
250 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
251 <option value="chorNOG">Chordata (chorNOG)</option>
252 <option value="chrNOG">Chromadorea (chrNOG)</option>
253 <option value="cloNOG">Clostridia (cloNOG)</option>
254 <option value="cocNOG">Coccidia (cocNOG)</option>
255 <option value="creNOG">Crenarchaeota (creNOG)</option>
256 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
257 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
258 <option value="cytNOG">Cytophagia (cytNOG)</option>
259 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
260 <option value="defNOG">Deferribacteres (defNOG)</option>
261 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
262 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
263 <option value="delNOG">delta/epsilon (delNOG)</option>
264 <option value="dipNOG">Diptera (dipNOG)</option>
265 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
266 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
267 <option value="droNOG">Drosophilidae (droNOG)</option>
268 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
269 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
270 <option value="euNOG">Eukaryotes (euNOG)</option>
271 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
272 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
273 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
274 <option value="fiNOG">Fishes (fiNOG)</option>
275 <option value="firmNOG">Firmicutes (firmNOG)</option>
276 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
277 <option value="fuNOG">Fungi (fuNOG)</option>
278 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
279 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
280 <option value="haeNOG">Haemosporida (haeNOG)</option>
281 <option value="halNOG">Halobacteria (halNOG)</option>
282 <option value="homNOG">Hominidae (homNOG)</option>
283 <option value="hymNOG">Hymenoptera (hymNOG)</option>
284 <option value="hypNOG">Hypocreales (hypNOG)</option>
285 <option value="inNOG">Insects (inNOG)</option>
286 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
287 <option value="lepNOG">Lepidoptera (lepNOG)</option>
288 <option value="lilNOG">Liliopsida (lilNOG)</option>
289 <option value="maNOG">Mammals (maNOG)</option>
290 <option value="magNOG">Magnaporthales (magNOG)</option>
291 <option value="meNOG">Animals (meNOG)</option>
292 <option value="metNOG">Methanobacteria (metNOG)</option>
293 <option value="methNOG">Methanococci (methNOG)</option>
294 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
295 <option value="necNOG">Nectriaceae (necNOG)</option>
296 <option value="negNOG">Negativicutes (negNOG)</option>
297 <option value="nemNOG">Nematodes (nemNOG)</option>
298 <option value="onyNOG">Onygenales (onyNOG)</option>
299 <option value="opiNOG">Opisthokonts (opiNOG)</option>
300 <option value="perNOG">Peronosporales (perNOG)</option>
301 <option value="plaNOG">Planctomycetes (plaNOG)</option>
302 <option value="pleNOG">Pleosporales (pleNOG)</option>
303 <option value="poaNOG">Poales (poaNOG)</option>
304 <option value="prNOG">Primates (prNOG)</option>
305 <option value="proNOG">Proteobacteria (proNOG)</option>
306 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
307 <option value="roNOG">Rodents (roNOG)</option>
308 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
309 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
310 <option value="sorNOG">Sordariales (sorNOG)</option>
311 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
312 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
313 <option value="spiNOG">Spirochaetes (spiNOG)</option>
314 <option value="spriNOG">Supraprimates (spriNOG)</option>
315 <option value="strNOG">Streptophyta (strNOG)</option>
316 <option value="synNOG">Synergistetes (synNOG)</option>
317 <option value="tenNOG">Tenericutes (tenNOG)</option>
318 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
319 <option value="theNOG">Thermoplasmata (theNOG)</option>
320 <option value="therNOG">Thermotogae (therNOG)</option>
321 <option value="thermNOG">Thermococci (thermNOG)</option>
322 <option value="treNOG">Tremellales (treNOG)</option>
323 <option value="veNOG">Vertebrates (veNOG)</option>
324 <option value="verNOG">Verrucomicrobia (verNOG)</option>
325 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
326 <option value="virNOG">Viridiplantae (virNOG)</option>
327 </param>
328 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
329 <option value="one2one">one2one</option>
330 <option value="many2one">many2one</option>
331 <option value="one2many">one2many</option>
332 <option value="many2many">many2many</option>
333 <option value="all" selected="true">all</option>
334 </param>
335 <param name="go_evidence" type="select"
336 label="Select the set of GO terms that should be used for annotation">
337 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
338 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
339 </param>
340 </section>
341 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
342 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
343 <help>
344 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
345 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
346 </help>
347 </param>
348 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
349 <help>
350 Min bit score expected when searching for seed eggNOG ortholog.
351 Queries not having a significant seed orthologs will not be annotated.
352 </help>
353 </param>
354 </section>
355 <section name="output_options" expanded="false" title="Output Options">
356 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
357 label="Exclude header lines and stats from output files"/>
358 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
359 label="Skip functional annotation, reporting only hits"/>
360 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
361 label="Output a file with the list of orthologs for each hits"/>
362 </section>
363 </inputs>
364 <outputs>
365 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
366 <actions>
367 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
368 </actions>
369 </data>
370 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
371 <filter>not output_options['no_annot']</filter>
372 <actions>
373 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>
374 </actions>
375 </data>
376 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits">
377 <filter>db['mode'] == 'hmmer'</filter>
378 <actions>
379 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
380 </actions>
381 </data>
382 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
383 <filter>output_options['report_orthologs']</filter>
384 <actions>
385 <action name="column_names" type="metadata" default="query_name,orthologs"/>
386 </actions>
387 </data>
388 </outputs>
389 <tests>
390 <test>
391 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
392 <param name="database" value="ENOG411CB2I"/>
393 <param name="mode" value="hmmer"/>
394 <param name="test" value="true"/>
395 <param name="eggnog_data" value="eggNOG_4.5"/>
396 <param name="no_annot" value="true"/>
397 <param name="no_file_comments" value="true"/>
398 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
399 </test>
400 <test>
401 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
402 <param name="eggnog_data" value="eggNOG_4.5"/> <!-- not passed in test, but required for test to work -->
403 <param name="no_annot" value="true"/>
404 <param name="mode" value="diamond"/>
405 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
406 </test>
407 </tests>
408 <help><![CDATA[
409
410 eggnog-mapper
411 =============
412 Overview
413 --------
414
415 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
416 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
417 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
418 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
419
420 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
421
422 Options
423 -------
424
425 ``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_.
426 HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences.
427
428
429 Outputs
430 -------
431
432 **hmm_hits**
433
434 For each query sequence, a list of significant
435 hits to eggNOG Orthologous Groups (OGs) is reported.
436 Each line in the file represents a hit, where evalue, bit-score,
437 query-coverage and the sequence coordinates of the match are reported.
438 If multiple hits exist for a given query, results are sorted by e-value.
439 Only returned when using HMMER mode.
440
441 **seed_orthologs**
442
443 each line in the file provides the best match of each query within the best Orthologous Group (OG)
444 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
445 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
446 If using the diamond search mode, seed orthologs are directly
447 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
448
449 **annotations**
450
451 This file provides final annotations of each query. Tab-delimited columns in the file are:
452
453 - ``query_name``: query sequence name
454 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
455 - ``seed_ortholog_evalue``: best protein match (e-value)
456 - ``seed_ortholog_score``: best protein match (bit-score)
457 - ``predicted_gene_name``: Predicted gene name for query sequences
458 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
459 - ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
460 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
461 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
462 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
463 - ``COG functional categories``: COG functional category inferred from best matching OG
464 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
465
466 ]]></help>
467 <citations>
468 <citation type="doi">10.1093/nar/gkv1248</citation>
469 </citations>
470 </tool>