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comparison eggnog_mapper.xml @ 13:844fa988236b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
author galaxyp
date Mon, 04 Sep 2023 12:47:09 +0000
parents 9d1fbff733cf
children
comparison
equal deleted inserted replaced
12:9d1fbff733cf 13:844fa988236b
1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>functional sequence annotation by orthology</description> 2 <description>functional sequence annotation by orthology</description>
3 <macros> 3 <macros>
4 <import>eggnog_macros.xml</import> 4 <import>eggnog_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_command"/> 7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #if $ortho_method.m == "no_search" 9 @MERGE_ANNOTATIONS@
10 cat
11 #for aht in $ortho_method.annotate_hits_table
12 $aht
13 #end for
14 > annotate_hits_table.tsv
15 &&
16 #end if
17 10
18 emapper.py 11 emapper.py
19 --data_dir '$eggnog_data.fields.path' 12 @DB_TOKEN@
20 -m '$ortho_method.m' 13 @ORTHO_SEARCH_TOKEN@
21
22 #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']:
23 -i '$ortho_method.input'
24 --itype '$ortho_method.input_trans.itype'
25 #if $ortho_method.input_trans.itype in ['CDS', 'genome', 'metagenome']:
26 $ortho_method.input_trans.translate
27 #end if
28 #if $ortho_method.input_trans.itype in ['genome', 'metagenome']:
29 --genepred $ortho_method.input_trans.genepred
30 #end if
31 #elif $ortho_method.m == "no_search"
32 --annotate_hits_table annotate_hits_table.tsv
33 #end if
34
35 #if $ortho_method.m == 'cache'
36 --cache '$ortho_method.cache'
37 #end if
38
39 #if $ortho_method.m in ['diamond', 'mmseqs']:
40 ## Diamond option
41 #if $ortho_method.m == "diamond":
42 --matrix '$ortho_method.matrix_gapcosts.matrix'
43 $ortho_method.matrix_gapcosts.gap_costs
44 --sensmode $ortho_method.sensmode
45 $ortho_method.dmnd_iterate
46 $ortho_method.dmnd_ignore_warnings
47 #elif $ortho_method.m == "mmseqs":
48 --start_sens $ortho_method.start_sens
49 --sens_steps $ortho_method.sens_steps
50 --final_sens $ortho_method.final_sens
51 #end if
52
53 ## Common options for search filtering (applies to diamond and mmseqs only)
54 #if str($ortho_method.query_cover):
55 --query_cover $ortho_method.query_cover
56 #end if
57 #if str($ortho_method.subject_cover):
58 --subject_cover $ortho_method.subject_cover
59 #end if
60 #if str($ortho_method.pident):
61 --pident $ortho_method.pident
62 #end if
63 #if str($ortho_method.evalue):
64 --evalue $ortho_method.evalue
65 #end if
66 #if str($ortho_method.score):
67 --score $ortho_method.score
68 #end if
69 #end if
70
71 #if $annotation_options.no_annot == "--no_annot" 14 #if $annotation_options.no_annot == "--no_annot"
72 --no_annot 15 --no_annot
73 #else 16 #else
74 #if str($annotation_options.seed_ortholog_evalue): 17 @ANNOTATION_TOKEN@
75 --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue
76 #end if
77 #if str($annotation_options.seed_ortholog_score):
78 --seed_ortholog_score $annotation_options.seed_ortholog_score
79 #end if
80 #if $annotation_options.tax_scope:
81 --tax_scope=$annotation_options.tax_scope
82 #end if
83 #if $annotation_options.target_orthologs:
84 --target_orthologs=$annotation_options.target_orthologs
85 #end if
86 #if $annotation_options.go_evidence:
87 --go_evidence=$annotation_options.go_evidence
88 #end if
89 #end if 18 #end if
90 $output_options.no_file_comments 19 $output_options.no_file_comments
91 $output_options.report_orthologs 20 $output_options.report_orthologs
92 $output_options.md5 21 $output_options.md5
93 --output='results' 22 --output='results'
94 --cpu "\${GALAXY_SLOTS:-4}" 23 --cpu "\${GALAXY_SLOTS:-4}"
95 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} 24 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
96 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} 25 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
97 ]]></command> 26 ]]></command>
98 <inputs> 27 <inputs>
99 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> 28 <expand macro="db_macro"/>
100 <options from_data_table="eggnog_mapper_db_versioned"> 29 <expand macro="ortho_full_macro"/>
101 <filter type="static_value" column="3" value="@IDX_VERSION@" />
102 </options>
103 </param>
104
105 <conditional name="ortho_method">
106 <param argument="-m" type="select" label="Method to search seed orthologs">
107 <option value="diamond" selected="true">Diamond</option>
108 <option value="mmseqs">MMseqs2</option>
109 <option value="no_search">Skip search stage: annotate an existing seed orthologs data set</option>
110 <option value="cache">Skip search stage: annotate based on cached annotations (see also --md5)</option>
111 </param>
112 <when value="diamond">
113 <expand macro="fasta_input"/>
114 <conditional name="matrix_gapcosts">
115 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
116 <option value="BLOSUM90">BLOSUM90</option>
117 <option value="BLOSUM80">BLOSUM80</option>
118 <option value="BLOSUM62" selected="true">BLOSUM62</option>
119 <option value="BLOSUM50">BLOSUM50</option>
120 <option value="BLOSUM45">BLOSUM45</option>
121 <option value="PAM250">PAM250</option>
122 <option value="PAM70">PAM70</option>
123 <option value="PAM30">PAM30</option>
124 </param>
125 <when value="BLOSUM90">
126 <param name="gap_costs" type="select" label="Gap Costs">
127 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
128 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
129 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
130 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
131 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
132 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
134 </param>
135 </when>
136 <when value="BLOSUM80">
137 <param name="gap_costs" type="select" label="Gap Costs">
138 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
139 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
140 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
141 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
142 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
143 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
144 </param>
145 </when>
146 <when value="BLOSUM62">
147 <param name="gap_costs" type="select" label="Gap Costs">
148 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
149 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
150 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
151 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
152 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
153 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
154 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
155 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
156 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
157 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
158 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
159 </param>
160 </when>
161 <when value="BLOSUM50">
162 <param name="gap_costs" type="select" label="Gap Costs">
163 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
164 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
165 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
166 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
167 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
168 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
169 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
170 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
171 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
172 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
173 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
174 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
175 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
176 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
177 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
178 </param>
179 </when>
180 <when value="BLOSUM45">
181 <param name="gap_costs" type="select" label="Gap Costs">
182 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
183 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
184 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
185 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
186 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
187 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
188 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
189 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
190 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
191 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
192 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
193 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
194 </param>
195 </when>
196 <when value="PAM250">
197 <param name="gap_costs" type="select" label="Gap Costs">
198 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
199 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
200 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
201 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
202 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
203 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
204 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
205 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
206 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
207 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
208 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
209 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
210 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
211 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
212 </param>
213 </when>
214 <when value="PAM70">
215 <param name="gap_costs" type="select" label="Gap Costs">
216 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
217 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
218 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
219 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
220 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
221 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
222 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
223 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
224 </param>
225 </when>
226 <when value="PAM30">
227 <param name="gap_costs" type="select" label="Gap Costs">
228 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
229 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
230 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
231 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
232 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
233 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
234 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
235 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
236 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
237 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
238 </param>
239 </when>
240 </conditional>
241 <param argument="--sensmode" type="select" label="Diamond's sensitivity mode">
242 <option value="default">default</option>
243 <option value="fast">fast</option>
244 <option value="mid-sensitive">mid-sensitive</option>
245 <option value="sensitive" selected="true">sensitive</option>
246 <option value="more-sensitive">more-sensitive</option>
247 <option value="very-sensitive">very-sensitive</option>
248 <option value="ultra-sensitive">ultra-sensitive</option>
249 </param>
250 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false"
251 label="Run diamond in iterative mode, up to the sensitivity level"/>
252 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false"
253 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/>
254 <expand macro="common_search_options"/>
255 </when>
256 <when value="mmseqs">
257 <expand macro="fasta_input"/>
258 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" />
259 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" />
260 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" />
261 <expand macro="common_search_options"/>
262 </when>
263 <when value="no_search">
264 <param argument="--annotate_hits_table" type="data" multiple="true" format="tabular" label="Seed orthologs">
265 <validator type="expression" message="No seed orthologs">value.metadata.columns == 11</validator>
266 <!-- would be cool to replace with this validator:
267 <validator type="expression" message="No seed orthologs">value.metadata.column_names == '@SEED_ORTHOLOG_COLUMNS@'.split()</validator>
268 but this does not work (yet) in tool tests since column_names can not be set in uploads -->
269 </param>
270 </when>
271 <when value="cache">
272 <expand macro="fasta_input"/>
273 <param argument="--cache" type="data" multiple="true" format="tabular" label="EggNOG Annotations with md5 hashes" help="Annotations computed with EggNOG mapper with enabled --md5 option">
274 <validator type="expression" message="No seed orthologs">value.metadata.columns == 22</validator>
275 </param>
276 <param name="output_no_annotations" type="boolean" checked="true" label="Output sequences without annotation" help="Produce an additional FASTA file with the sequences of queries for which an existing annotation was not found using cache mode. This file can be used as input of another eggNOG-mapper run without using the cache, trying to annotate the sequences."/>
277 </when>
278 </conditional>
279
280 <conditional name="annotation_options"> 30 <conditional name="annotation_options">
281 <param argument="--no_annot" type="select" label="Annotate seed orthologs"> 31 <param argument="--no_annot" type="select" label="Annotate seed orthologs">
282 <option value="">Yes</option> 32 <option value="">Yes</option>
283 <option value="--no_annot">No</option> 33 <option value="--no_annot">No</option>
284 </param> 34 </param>
285 <when value=""> 35 <when value="">
286 <param argument="--seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> 36 <expand macro="annotation_options_macro"/>
287 <help>
288 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
289 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
290 </help>
291 </param>
292 <param argument="--seed_ortholog_score" type="float" optional="true" min="0" label="Minimum bit score threshold">
293 <help>
294 Min bit score expected when searching for seed eggNOG ortholog.
295 Queries not having a significant seed orthologs will not be annotated.
296 </help>
297 </param>
298 <param argument="--tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
299 <param argument="--target_orthologs" type="select" label="target orthologs for functional transfer">
300 <option value="one2one">one2one</option>
301 <option value="many2one">many2one</option>
302 <option value="one2many">one2many</option>
303 <option value="many2many">many2many</option>
304 <option value="all" selected="true">all</option>
305 </param>
306 <param argument="--go_evidence" type="select"
307 label="Select the set of GO terms that should be used for annotation">
308 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
309 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
310 <option value="all" selected="true">All (experimental + non-electronic)</option>
311 </param>
312 </when> 37 </when>
313 <when value="--no_annot"/> 38 <when value="--no_annot"/>
314 </conditional> 39 </conditional>
315 40
316 <section name="output_options" expanded="false" title="Output Options"> 41 <expand macro="output_options_annotate_macro"/>
317 <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
318 label="Exclude header lines and stats from output files"/>
319 <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
320 label="Output a file with the list of orthologs for each hits"/>
321 <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false"
322 label="Add md5 hash of each query to annotations"/>
323 </section>
324 </inputs> 42 </inputs>
325 <outputs> 43 <outputs>
326 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs"> 44 <expand macro="ortho_search_output_macro"/>
327 <filter>ortho_method['m'] not in ['no_search', 'cache']</filter> 45 <expand macro="annotation_output_macro">
328 <actions>
329 <action name="column_names" type="metadata" default="@SEED_ORTHOLOG_COLUMNS@"/>
330 </actions>
331 </data>
332 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
333 <filter>annotation_options['no_annot'] == ''</filter> 46 <filter>annotation_options['no_annot'] == ''</filter>
334 <actions> 47 </expand>
335 <conditional name="output_options.md5"> 48 <expand macro="annotation_orthologs_output_macro"/>
336 <when value="True">
337 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
338 </when>
339 <when value="False">
340 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
341 </when>
342 </conditional>
343 </actions>
344 </data>
345 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
346 <filter>ortho_method['m'] != 'cache' and output_options['report_orthologs']</filter>
347 <actions>
348 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
349 </actions>
350 </data>
351 <data name="no_annotations" format="fasta" label="${tool.name} on ${on_string}: Sequences wo annotation" from_work_dir="results.emapper.no_annotations.fasta">
352 <filter>ortho_method['m'] == 'cache' and output_options['output_no_annotations']</filter>
353 </data>
354 </outputs> 49 </outputs>
355 <tests> 50 <tests>
356 <!-- test producing only seed orthologs--> 51 <!-- test producing only seed orthologs-->
357 <test expect_num_outputs="1"> 52 <test expect_num_outputs="1">
358 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> 53 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
361 </conditional> 56 </conditional>
362 <conditional name="annotation_options"> 57 <conditional name="annotation_options">
363 <param name="no_annot" value="--no_annot"/> 58 <param name="no_annot" value="--no_annot"/>
364 </conditional> 59 </conditional>
365 <section name="output_options"> 60 <section name="output_options">
366 <param name="no_file_comments" value="true"/>
367 </section> 61 </section>
368 <expand macro="seed_orthologs_assertion"/> 62 <expand macro="seed_orthologs_assertion"/>
369 <expand macro="stdout_assertion"/> 63 <expand macro="stdout_assertion"/>
370 </test> 64 </test>
371 65
380 </conditional> 74 </conditional>
381 <conditional name="annotation_options"> 75 <conditional name="annotation_options">
382 </conditional> 76 </conditional>
383 <section name="output_options"> 77 <section name="output_options">
384 <param name="report_orthologs" value="true"/> 78 <param name="report_orthologs" value="true"/>
385 <param name="no_file_comments" value="true"/>
386 </section> 79 </section>
387 <expand macro="annotations_assertion"/> 80 <expand macro="annotations_assertion"/>
388 <expand macro="annotations_orthologs_assertion"/> 81 <expand macro="annotations_orthologs_assertion"/>
389 <expand macro="stdout_assertion"/> 82 <expand macro="stdout_assertion"/>
390 </test> 83 </test>
395 <conditional name="ortho_method"> 88 <conditional name="ortho_method">
396 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 89 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
397 </conditional> 90 </conditional>
398 <section name="output_options"> 91 <section name="output_options">
399 <param name="report_orthologs" value="true"/> 92 <param name="report_orthologs" value="true"/>
400 <param name="no_file_comments" value="true"/> 93 <param name="no_file_comments" value="false"/>
401 <param name="md5" value="true"/> 94 <param name="md5" value="true"/>
402 </section> 95 </section>
403 <expand macro="seed_orthologs_assertion"/> 96 <expand macro="seed_orthologs_assertion" nocomments="false"/>
404 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/> 97 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+" nocomments="false"/>
405 <expand macro="annotations_orthologs_assertion"/> 98 <expand macro="annotations_orthologs_assertion" nocomments="false"/>
406 <expand macro="stdout_assertion"/> 99 <expand macro="stdout_assertion"/>
407 </test> 100 </test>
408 101
409 <!-- test using chached annotations from previous run --> 102 <!-- test using chached annotations from previous run -->
410 <test expect_num_outputs="2"> 103 <test expect_num_outputs="2">
414 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 107 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
415 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/> 108 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
416 </conditional> 109 </conditional>
417 <section name="output_options"> 110 <section name="output_options">
418 <param name="report_orthologs" value="true"/> 111 <param name="report_orthologs" value="true"/>
419 <param name="no_file_comments" value="true"/>
420 <param name="md5" value="true"/> 112 <param name="md5" value="true"/>
421 </section> 113 </section>
422 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/> 114 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
423 <output name="no_annotations" ftype="fasta"> 115 <output name="no_annotations" ftype="fasta">
424 <assert_contents> 116 <assert_contents>
437 <section name="annotation_options"> 129 <section name="annotation_options">
438 <param name="tax_scope" value="651137" /> 130 <param name="tax_scope" value="651137" />
439 </section> 131 </section>
440 <section name="output_options"> 132 <section name="output_options">
441 <param name="report_orthologs" value="true"/> 133 <param name="report_orthologs" value="true"/>
442 <param name="no_file_comments" value="true"/>
443 </section> 134 </section>
444 <expand macro="seed_orthologs_assertion"/> 135 <expand macro="seed_orthologs_assertion"/>
445 <expand macro="annotations_assertion"/> 136 <expand macro="annotations_assertion"/>
446 <expand macro="annotations_orthologs_assertion"/> 137 <expand macro="annotations_orthologs_assertion"/>
447 <expand macro="stdout_assertion"> 138 <expand macro="stdout_assertion">
457 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 148 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
458 <param name="sensmode" value="fast" /> 149 <param name="sensmode" value="fast" />
459 </conditional> 150 </conditional>
460 <section name="output_options"> 151 <section name="output_options">
461 <param name="report_orthologs" value="true"/> 152 <param name="report_orthologs" value="true"/>
462 <param name="no_file_comments" value="true"/>
463 </section> 153 </section>
464 <expand macro="seed_orthologs_assertion"/> 154 <expand macro="seed_orthologs_assertion"/>
465 <expand macro="annotations_assertion"/> 155 <expand macro="annotations_assertion"/>
466 <expand macro="annotations_orthologs_assertion"/> 156 <expand macro="annotations_orthologs_assertion"/>
467 <expand macro="stdout_assertion"> 157 <expand macro="stdout_assertion">
500 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_. 190 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
501 191
502 Outputs 192 Outputs
503 ------- 193 -------
504 194
505 **seed_orthologs** 195 @HELP_SEARCH_OUTPUTS@
506 196
507 each line in the file provides the best match of each query within the best Orthologous Group (OG) 197 @HELP_ANNOTATION_OUTPUTS@
508 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. 198
509 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. 199
510 If using the diamond search mode, seed orthologs are directly
511 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
512
513 **annotations**
514
515 This file provides final annotations of each query. Tab-delimited columns in the file are:
516
517 - ``query_name``: query sequence name
518 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
519 - ``seed_ortholog_evalue``: best protein match (e-value)
520 - ``seed_ortholog_score``: best protein match (bit-score)
521 - ``predicted_taxonomic_group``
522 - ``predicted_protein_name``: Predicted protein name for query sequences
523 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
524 - ``EC_number``
525 - ``KEGG_KO``
526 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
527 - ``KEGG_Module``
528 - ``KEGG_Reaction``
529 - ``KEGG_rclass``
530 - ``BRITE``
531 - ``KEGG_TC``
532 - ``CAZy``
533 - ``BiGG_Reactions``
534 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
535 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
536 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
537 - ``COG_functional_categories``: COG functional category inferred from best matching OG
538 - ``eggNOG_free_text_description``
539 200
540 **Recommentation for large input data** 201 **Recommentation for large input data**
541 202
542 EggNOG-mapper consists of two phases 203 EggNOG-mapper consists of two phases
543 204
556 217
557 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs) 218 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
558 219
559 Another alternative is to use cached annotations (produced in a run with --md5 enabled). 220 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
560 221
561
562 ]]></help> 222 ]]></help>
563 <expand macro="citations"/> 223 <expand macro="citations"/>
564 </tool> 224 </tool>