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comparison eggnog_mapper.xml @ 12:9d1fbff733cf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
author galaxyp
date Tue, 19 Jul 2022 15:14:52 +0000
parents 5a30ae278db0
children 844fa988236b
comparison
equal deleted inserted replaced
11:5a30ae278db0 12:9d1fbff733cf
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"
10 cat
11 #for aht in $ortho_method.annotate_hits_table
12 $aht
13 #end for
14 > annotate_hits_table.tsv
15 &&
16 #end if
17
9 emapper.py 18 emapper.py
10 --data_dir '$eggnog_data.fields.path' 19 --data_dir '$eggnog_data.fields.path'
11 -m '$seed_ortho_options.ortho_method.m' 20 -m '$ortho_method.m'
12 --itype '${input_trans.itype}' 21
13 #if $input_trans.itype in ['CDS', 'genome', 'metagenome']: 22 #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']:
14 $input_trans.translate 23 -i '$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
15 #end if 33 #end if
16 #if $input_trans.itype in ['genome', 'metagenome']: 34
17 --genepred $input_trans.genepred 35 #if $ortho_method.m == 'cache'
36 --cache '$ortho_method.cache'
18 #end if 37 #end if
19 38
20 ## Diamond option 39 #if $ortho_method.m in ['diamond', 'mmseqs']:
21 #if $seed_ortho_options.ortho_method.m == "diamond": 40 ## Diamond option
22 --matrix '$seed_ortho_options.ortho_method.matrix_gapcosts.matrix' 41 #if $ortho_method.m == "diamond":
23 $seed_ortho_options.ortho_method.matrix_gapcosts.gap_costs 42 --matrix '$ortho_method.matrix_gapcosts.matrix'
24 --sensmode $seed_ortho_options.ortho_method.sensmode 43 $ortho_method.matrix_gapcosts.gap_costs
25 $seed_ortho_options.ortho_method.dmnd_iterate 44 --sensmode $ortho_method.sensmode
26 $seed_ortho_options.ortho_method.dmnd_ignore_warnings 45 $ortho_method.dmnd_iterate
27 #elif $seed_ortho_options.ortho_method.m == "mmseqs": 46 $ortho_method.dmnd_ignore_warnings
28 --start_sens $seed_ortho_options.ortho_method.start_sens 47 #elif $ortho_method.m == "mmseqs":
29 --sens_steps $seed_ortho_options.ortho_method.sens_steps 48 --start_sens $ortho_method.start_sens
30 --final_sens $seed_ortho_options.ortho_method.final_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
31 #end if 69 #end if
32 70
33 ## Common options for search filtering 71 #if $annotation_options.no_annot == "--no_annot"
34 #if $seed_ortho_options.query_cover: 72 --no_annot
35 --query_cover $seed_ortho_options.query_cover 73 #else
36 #end if 74 #if str($annotation_options.seed_ortholog_evalue):
37 #if $seed_ortho_options.subject_cover: 75 --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue
38 --subject_cover $seed_ortho_options.subject_cover 76 #end if
39 #end if 77 #if str($annotation_options.seed_ortholog_score):
40 #if $seed_ortho_options.pident: 78 --seed_ortholog_score $annotation_options.seed_ortholog_score
41 --pident $seed_ortho_options.pident 79 #end if
42 #end if 80 #if $annotation_options.tax_scope:
43 81 --tax_scope=$annotation_options.tax_scope
44 #if $annotation_options.tax_scope: 82 #end if
45 --tax_scope=$annotation_options.tax_scope 83 #if $annotation_options.target_orthologs:
46 #end if 84 --target_orthologs=$annotation_options.target_orthologs
47 #if $annotation_options.target_orthologs: 85 #end if
48 --target_orthologs=$annotation_options.target_orthologs 86 #if $annotation_options.go_evidence:
49 #end if 87 --go_evidence=$annotation_options.go_evidence
50 #if $annotation_options.go_evidence: 88 #end if
51 --go_evidence=$annotation_options.go_evidence
52 #end if
53 #if $seed_ortholog_options.seed_ortholog_evalue:
54 --evalue=$seed_ortholog_options.seed_ortholog_evalue
55 #end if
56 #if str($seed_ortholog_options.seed_ortholog_score):
57 --score=$seed_ortholog_options.seed_ortholog_score
58 #end if 89 #end if
59 $output_options.no_file_comments 90 $output_options.no_file_comments
60 $output_options.no_annot
61 $output_options.report_orthologs 91 $output_options.report_orthologs
92 $output_options.md5
62 --output='results' 93 --output='results'
63 -i '${input}'
64 --cpu "\${GALAXY_SLOTS:-4}" 94 --cpu "\${GALAXY_SLOTS:-4}"
95 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
96 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
65 ]]></command> 97 ]]></command>
66 <inputs> 98 <inputs>
67 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
68 <conditional name="input_trans">
69 <param argument="--itype" type="select" label="Type of sequences">
70 <option value="proteins" selected="true">proteins</option>
71 <option value="CDS">CDS</option>
72 <option value="genome">genome</option>
73 <option value="metagenome">metagenome</option>
74 </param>
75 <when value="proteins"/>
76 <when value="CDS">
77 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
78 label="Translate CDS to proteins before search"/>
79 </when>
80 <when value="genome">
81 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
82 label="Translate predicted CDS from blastx hits to proteins"/>
83 <param argument="--genepred" type="select" label="Type of sequences">
84 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
85 <option value="prodigal" selected="true">Performed using Prodigal</option>
86 </param>
87 </when>
88 <when value="metagenome">
89 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
90 label="Translate predicted CDS from blastx hits to proteins"/>
91 <param argument="--genepred" type="select" label="Type of sequences">
92 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
93 <option value="prodigal" selected="true">Performed using Prodigal</option>
94 </param>
95 </when>
96 </conditional>
97 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> 99 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
98 <options from_data_table="eggnog_mapper_db_versioned"> 100 <options from_data_table="eggnog_mapper_db_versioned">
99 <filter type="static_value" column="3" value="@IDX_VERSION@" /> 101 <filter type="static_value" column="3" value="@IDX_VERSION@" />
100 </options> 102 </options>
101 </param> 103 </param>
102 104
103 <section name="seed_ortho_options" expanded="true" title="Seed orthologs search options"> 105 <conditional name="ortho_method">
104 <conditional name="ortho_method"> 106 <param argument="-m" type="select" label="Method to search seed orthologs">
105 <param argument="-m" type="select" label="Method to search seed orthologs"> 107 <option value="diamond" selected="true">Diamond</option>
106 <option value="diamond" selected="true">Diamond</option> 108 <option value="mmseqs">MMseqs2</option>
107 <option value="mmseqs">MMseqs2</option> 109 <option value="no_search">Skip search stage: annotate an existing seed orthologs data set</option>
108 </param> 110 <option value="cache">Skip search stage: annotate based on cached annotations (see also --md5)</option>
109 <when value="diamond"> 111 </param>
110 <conditional name="matrix_gapcosts"> 112 <when value="diamond">
111 <param argument="--matrix" type="select" label="Scoring matrix and gap costs"> 113 <expand macro="fasta_input"/>
112 <option value="BLOSUM90">BLOSUM90</option> 114 <conditional name="matrix_gapcosts">
113 <option value="BLOSUM80">BLOSUM80</option> 115 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
114 <option value="BLOSUM62" selected="true">BLOSUM62</option> 116 <option value="BLOSUM90">BLOSUM90</option>
115 <option value="BLOSUM50">BLOSUM50</option> 117 <option value="BLOSUM80">BLOSUM80</option>
116 <option value="BLOSUM45">BLOSUM45</option> 118 <option value="BLOSUM62" selected="true">BLOSUM62</option>
117 <option value="PAM250">PAM250</option> 119 <option value="BLOSUM50">BLOSUM50</option>
118 <option value="PAM70">PAM70</option> 120 <option value="BLOSUM45">BLOSUM45</option>
119 <option value="PAM30">PAM30</option> 121 <option value="PAM250">PAM250</option>
120 </param> 122 <option value="PAM70">PAM70</option>
121 <when value="BLOSUM90"> 123 <option value="PAM30">PAM30</option>
122 <param name="gap_costs" type="select" label="Gap Costs">
123 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
124 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
125 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
126 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
127 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
128 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
129 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
130 </param>
131 </when>
132 <when value="BLOSUM80">
133 <param name="gap_costs" type="select" label="Gap Costs">
134 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
135 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
136 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
137 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
138 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
139 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
140 </param>
141 </when>
142 <when value="BLOSUM62">
143 <param name="gap_costs" type="select" label="Gap Costs">
144 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
145 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
146 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
147 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
148 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
149 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
150 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
151 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
152 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
153 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
154 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
155 </param>
156 </when>
157 <when value="BLOSUM50">
158 <param name="gap_costs" type="select" label="Gap Costs">
159 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
160 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
161 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
162 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
163 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
164 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
165 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
166 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
167 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
168 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
169 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
170 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
171 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
172 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
173 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
174 </param>
175 </when>
176 <when value="BLOSUM45">
177 <param name="gap_costs" type="select" label="Gap Costs">
178 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
179 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
180 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
181 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
182 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
183 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
184 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
185 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
186 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
187 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
188 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
189 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
190 </param>
191 </when>
192 <when value="PAM250">
193 <param name="gap_costs" type="select" label="Gap Costs">
194 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
195 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
196 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
197 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
198 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
199 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
200 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
201 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
202 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
203 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
204 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
205 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
206 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
207 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
208 </param>
209 </when>
210 <when value="PAM70">
211 <param name="gap_costs" type="select" label="Gap Costs">
212 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
213 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
214 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
215 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
216 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
217 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
218 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
219 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
220 </param>
221 </when>
222 <when value="PAM30">
223 <param name="gap_costs" type="select" label="Gap Costs">
224 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
225 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
226 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
227 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
228 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
229 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
230 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
231 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
232 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
233 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
234 </param>
235 </when>
236 </conditional>
237 <param name="sensmode" type="select" label="Gap Costs">
238 <option value="default">default</option>
239 <option value="fast">fast</option>
240 <option value="mid-sensitive">mid-sensitive</option>
241 <option value="sensitive" selected="true">sensitive</option>
242 <option value="more-sensitive">more-sensitive</option>
243 <option value="very-sensitive">very-sensitive</option>
244 <option value="ultra-sensitive">ultra-sensitive</option>
245 </param> 124 </param>
246 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false" 125 <when value="BLOSUM90">
247 label="Run diamond in iterative mode, up to the sensitivity level"/> 126 <param name="gap_costs" type="select" label="Gap Costs">
248 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false" 127 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
249 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/> 128 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
250 </when> 129 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
251 <when value="mmseqs"> 130 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
252 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" /> 131 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
253 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" /> 132 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
254 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" /> 133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
255 </when> 134 </param>
256 </conditional> 135 </when>
257 136 <when value="BLOSUM80">
258 <param argument="--query_cover" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" /> 137 <param name="gap_costs" type="select" label="Gap Costs">
259 <param argument="--subject_cover" type="integer" optional="true" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" /> 138 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
260 <param argument="--pident" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of identity" /> 139 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
261 </section> 140 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
262 141 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
263 <section name="annotation_options" expanded="false" title="Annotation Options"> 142 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
264 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" /> 143 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
265 <param name="target_orthologs" type="select" label="target orthologs for functional transfer"> 144 </param>
266 <option value="one2one">one2one</option> 145 </when>
267 <option value="many2one">many2one</option> 146 <when value="BLOSUM62">
268 <option value="one2many">one2many</option> 147 <param name="gap_costs" type="select" label="Gap Costs">
269 <option value="many2many">many2many</option> 148 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
270 <option value="all" selected="true">all</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">
281 <param argument="--no_annot" type="select" label="Annotate seed orthologs">
282 <option value="">Yes</option>
283 <option value="--no_annot">No</option>
271 </param> 284 </param>
272 <param name="go_evidence" type="select" 285 <when value="">
273 label="Select the set of GO terms that should be used for annotation"> 286 <param argument="--seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
274 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option> 287 <help>
275 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option> 288 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
276 <option value="all" selected="true">All (experimental + non-electronic)</option> 289 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
277 </param> 290 </help>
278 </section> 291 </param>
279 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options"> 292 <param argument="--seed_ortholog_score" type="float" optional="true" min="0" label="Minimum bit score threshold">
280 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> 293 <help>
281 <help> 294 Min bit score expected when searching for seed eggNOG ortholog.
282 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. 295 Queries not having a significant seed orthologs will not be annotated.
283 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated. 296 </help>
284 </help> 297 </param>
285 </param> 298 <param argument="--tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
286 <param name="seed_ortholog_score" type="integer" optional="true" min="0" label="Minimum bit score threshold"> 299 <param argument="--target_orthologs" type="select" label="target orthologs for functional transfer">
287 <help> 300 <option value="one2one">one2one</option>
288 Min bit score expected when searching for seed eggNOG ortholog. 301 <option value="many2one">many2one</option>
289 Queries not having a significant seed orthologs will not be annotated. 302 <option value="one2many">one2many</option>
290 </help> 303 <option value="many2many">many2many</option>
291 </param> 304 <option value="all" selected="true">all</option>
292 </section> 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>
313 <when value="--no_annot"/>
314 </conditional>
315
293 <section name="output_options" expanded="false" title="Output Options"> 316 <section name="output_options" expanded="false" title="Output Options">
294 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true" 317 <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
295 label="Exclude header lines and stats from output files"/> 318 label="Exclude header lines and stats from output files"/>
296 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false" 319 <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
297 label="Skip functional annotation, reporting only hits"/>
298 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
299 label="Output a file with the list of orthologs for each hits"/> 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"/>
300 </section> 323 </section>
301 </inputs> 324 </inputs>
302 <outputs> 325 <outputs>
303 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs"> 326 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
327 <filter>ortho_method['m'] not in ['no_search', 'cache']</filter>
304 <actions> 328 <actions>
305 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov"/> 329 <action name="column_names" type="metadata" default="@SEED_ORTHOLOG_COLUMNS@"/>
306 </actions> 330 </actions>
307 </data> 331 </data>
308 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations"> 332 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
309 <filter>not output_options['no_annot']</filter> 333 <filter>annotation_options['no_annot'] == ''</filter>
310 <actions> 334 <actions>
311 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/> 335 <conditional name="output_options.md5">
336 <when value="True">
337 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
338 </when>
339 <when value="False">
340 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
341 </when>
342 </conditional>
312 </actions> 343 </actions>
313 </data> 344 </data>
314 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs"> 345 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
315 <filter>output_options['report_orthologs']</filter> 346 <filter>ortho_method['m'] != 'cache' and output_options['report_orthologs']</filter>
316 <actions> 347 <actions>
317 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/> 348 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
318 </actions> 349 </actions>
319 </data> 350 </data>
351 <data name="no_annotations" format="fasta" label="${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>
320 </outputs> 354 </outputs>
321 <tests> 355 <tests>
356 <!-- test producing only seed orthologs-->
322 <test expect_num_outputs="1"> 357 <test expect_num_outputs="1">
323 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
324 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> 358 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
325 <param name="no_annot" value="true"/> 359 <conditional name="ortho_method">
326 <param name="no_file_comments" value="true"/> 360 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
327 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> 361 </conditional>
362 <conditional name="annotation_options">
363 <param name="no_annot" value="--no_annot"/>
364 </conditional>
365 <section name="output_options">
366 <param name="no_file_comments" value="true"/>
367 </section>
368 <expand macro="seed_orthologs_assertion"/>
328 <expand macro="stdout_assertion"/> 369 <expand macro="stdout_assertion"/>
329 </test> 370 </test>
330 <test expect_num_outputs="3"> 371
331 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 372 <!-- test producing annotations form seed orthologs -->
373 <test expect_num_outputs="2">
332 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 374 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
333 <param name="report_orthologs" value="true"/> 375 <conditional name="ortho_method">
334 <param name="no_file_comments" value="true"/> 376 <param name="m" value="no_search"/>
335 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> 377 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
336 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> 378 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
337 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> 379 </param>
380 </conditional>
381 <conditional name="annotation_options">
382 </conditional>
383 <section name="output_options">
384 <param name="report_orthologs" value="true"/>
385 <param name="no_file_comments" value="true"/>
386 </section>
387 <expand macro="annotations_assertion"/>
388 <expand macro="annotations_orthologs_assertion"/>
338 <expand macro="stdout_assertion"/> 389 <expand macro="stdout_assertion"/>
339 </test> 390 </test>
391
392 <!-- test producing seed orthologs and annotations at once (ie the same as the previous two tests but in a single tool run) -->
340 <test expect_num_outputs="3"> 393 <test expect_num_outputs="3">
341 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
342 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 394 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
343 <param name="report_orthologs" value="true"/> 395 <conditional name="ortho_method">
344 <param name="no_file_comments" value="true"/> 396 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
397 </conditional>
398 <section name="output_options">
399 <param name="report_orthologs" value="true"/>
400 <param name="no_file_comments" value="true"/>
401 <param name="md5" value="true"/>
402 </section>
403 <expand macro="seed_orthologs_assertion"/>
404 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
405 <expand macro="annotations_orthologs_assertion"/>
406 <expand macro="stdout_assertion"/>
407 </test>
408
409 <!-- test using chached annotations from previous run -->
410 <test expect_num_outputs="2">
411 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
412 <conditional name="ortho_method">
413 <param name="m" value="cache"/>
414 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
415 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
416 </conditional>
417 <section name="output_options">
418 <param name="report_orthologs" value="true"/>
419 <param name="no_file_comments" value="true"/>
420 <param name="md5" value="true"/>
421 </section>
422 <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">
424 <assert_contents>
425 <has_n_lines n="0"/>
426 </assert_contents>
427 </output>
428 <expand macro="stdout_assertion"/>
429 </test>
430
431 <!-- test setting tax scope-->
432 <test expect_num_outputs="3">
433 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
434 <conditional name="ortho_method">
435 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
436 </conditional>
345 <section name="annotation_options"> 437 <section name="annotation_options">
346 <param name="tax_scope" value="651137" /> 438 <param name="tax_scope" value="651137" />
347 </section> 439 </section>
348 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> 440 <section name="output_options">
349 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> 441 <param name="report_orthologs" value="true"/>
350 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> 442 <param name="no_file_comments" value="true"/>
351 <expand macro="stdout_assertion"/> 443 </section>
444 <expand macro="seed_orthologs_assertion"/>
445 <expand macro="annotations_assertion"/>
446 <expand macro="annotations_orthologs_assertion"/>
447 <expand macro="stdout_assertion">
448 <has_text text="--tax_scope=651137"/>
449 </expand>
352 </test> 450 </test>
451
452 <!-- test setting a diamond option-->
353 <test expect_num_outputs="3"> 453 <test expect_num_outputs="3">
354 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
355 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 454 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
356 <section name="seed_ortho_options"> 455 <conditional name="ortho_method">
357 <conditional name="ortho_method"> 456 <param name="m" value="diamond" />
358 <param name="m" value="diamond" /> 457 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
359 <param name="sensmode" value="fast" /> 458 <param name="sensmode" value="fast" />
360 </conditional> 459 </conditional>
361 </section> 460 <section name="output_options">
362 <param name="report_orthologs" value="true"/> 461 <param name="report_orthologs" value="true"/>
363 <param name="no_file_comments" value="true"/> 462 <param name="no_file_comments" value="true"/>
364 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> 463 </section>
365 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> 464 <expand macro="seed_orthologs_assertion"/>
366 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> 465 <expand macro="annotations_assertion"/>
367 <expand macro="stdout_assertion"/> 466 <expand macro="annotations_orthologs_assertion"/>
467 <expand macro="stdout_assertion">
468 <has_text text="--sensmode fast"/>
469 </expand>
368 </test> 470 </test>
369 <!-- not enabled as it requires a specific .db file, hard to minimize --> 471 <!-- not enabled as it requires a specific .db file, hard to minimize -->
370 <!--test> 472 <!--test>
473 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
371 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 474 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
372 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
373 <section name="seed_ortho_options"> 475 <section name="seed_ortho_options">
374 <conditional name="ortho_method"> 476 <conditional name="ortho_method">
375 <param name="m" value="mmseqs" /> 477 <param name="m" value="mmseqs" />
376 <param name="start_sens" value="4" /> 478 <param name="start_sens" value="4" />
377 </conditional> 479 </conditional>
433 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups 535 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
434 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs) 536 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
435 - ``COG_functional_categories``: COG functional category inferred from best matching OG 537 - ``COG_functional_categories``: COG functional category inferred from best matching OG
436 - ``eggNOG_free_text_description`` 538 - ``eggNOG_free_text_description``
437 539
540 **Recommentation for large input data**
541
542 EggNOG-mapper consists of two phases
543
544 1. finding seed orthologous sequences (compute intensive)
545 2. expanding annotations (IO intensive)
546
547 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
548 both phases are executed within one tool run.
549
550 For large input FASTA datasets in can be favourable to split this in two separate
551 tool runs as follows:
552
553 1. Split the FASTA (e.g. 1M seqs per data set)
554 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
555 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
556
557 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
558
559 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
560
561
438 ]]></help> 562 ]]></help>
439 <expand macro="citations"/> 563 <expand macro="citations"/>
440 </tool> 564 </tool>