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comparison eggnog_mapper.xml @ 8:96cac424c870 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
author galaxyp
date Tue, 25 Jan 2022 13:51:50 +0000
parents 4e4c6329f6cd
children 63662ae295d6
comparison
equal deleted inserted replaced
7:4e4c6329f6cd 8:96cac424c870
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 emapper.py 9 emapper.py
10 --data_dir '$eggnog_data.fields.path' 10 --data_dir '$eggnog_data.fields.path'
11 -m diamond 11 -m '$seed_ortho_options.ortho_method.m'
12 $translate 12 --itype '${input_trans.itype}'
13 #if $input_trans.itype in ['CDS', 'genome', 'metagenome']:
14 $input_trans.translate
15 #end if
16 #if $input_trans.itype in ['genome', 'metagenome']:
17 $input_trans.genepred
18 #end if
13 19
14 ## Diamond option 20 ## Diamond option
15 --matrix '$diamond.matrix_gapcosts.matrix' 21 #if $seed_ortho_options.ortho_method.m == "diamond":
16 $diamond.matrix_gapcosts.gap_costs 22 --matrix '$seed_ortho_options.ortho_method.matrix_gapcosts.matrix'
17 --query-cover $diamond.query_cover 23 $seed_ortho_options.ortho_method.matrix_gapcosts.gap_costs
18 --subject-cover $diamond.subject_cover 24 --sensmode $seed_ortho_options.ortho_method.sensmode
25 $seed_ortho_options.ortho_method.dmnd_iterate
26 $seed_ortho_options.ortho_method.dmnd_ignore_warnings
27 #elif $seed_ortho_options.ortho_method.m == "mmseqs":
28 --start_sens $seed_ortho_options.ortho_method.start_sens
29 --sens_steps $seed_ortho_options.ortho_method.sens_steps
30 --final_sens $seed_ortho_options.ortho_method.final_sens
31 #end if
32
33 ## Common options for search filtering
34 #if $seed_ortho_options.query_cover:
35 --query_cover $seed_ortho_options.query_cover
36 #end if
37 #if $seed_ortho_options.subject_cover:
38 --subject_cover $seed_ortho_options.subject_cover
39 #end if
40 #if $seed_ortho_options.pident:
41 --pident $seed_ortho_options.pident
42 #end if
19 43
20 #if $annotation_options.tax_scope: 44 #if $annotation_options.tax_scope:
21 --tax_scope=$annotation_options.tax_scope 45 --tax_scope=$annotation_options.tax_scope
22 #end if 46 #end if
23 #if $annotation_options.target_orthologs: 47 #if $annotation_options.target_orthologs:
25 #end if 49 #end if
26 #if $annotation_options.go_evidence: 50 #if $annotation_options.go_evidence:
27 --go_evidence=$annotation_options.go_evidence 51 --go_evidence=$annotation_options.go_evidence
28 #end if 52 #end if
29 #if $seed_ortholog_options.seed_ortholog_evalue: 53 #if $seed_ortholog_options.seed_ortholog_evalue:
30 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue 54 --evalue=$seed_ortholog_options.seed_ortholog_evalue
31 #end if 55 #end if
32 #if str($seed_ortholog_options.seed_ortholog_score): 56 #if str($seed_ortholog_options.seed_ortholog_score):
33 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score 57 --score=$seed_ortholog_options.seed_ortholog_score
34 #end if 58 #end if
35 $output_options.no_file_comments 59 $output_options.no_file_comments
36 $output_options.no_annot 60 $output_options.no_annot
37 $output_options.report_orthologs 61 $output_options.report_orthologs
38 --output='results' 62 --output='results'
39 -i '${input}' 63 -i '${input}'
40 --cpu "\${GALAXY_SLOTS:-4}" 64 --cpu "\${GALAXY_SLOTS:-4}"
41 ]]></command> 65 ]]></command>
42 <inputs> 66 <inputs>
43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> 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" selected="true">Inferred from Diamond/MMseqs2 blastx hits</option>
85 <option value="prodigal">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" selected="true">Inferred from Diamond/MMseqs2 blastx hits</option>
93 <option value="prodigal">Performed using Prodigal</option>
94 </param>
95 </when>
96 </conditional>
44 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> 97 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
45 <options from_data_table="eggnog_mapper_db_versioned"> 98 <options from_data_table="eggnog_mapper_db_versioned">
46 <filter type="static_value" column="3" value="@IDX_VERSION@" /> 99 <filter type="static_value" column="3" value="@IDX_VERSION@" />
47 </options> 100 </options>
48 </param> 101 </param>
49 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" 102
50 label="Are these coding DNA sequences that need to be translated?"/> 103 <section name="seed_ortho_options" expanded="true" title="Seed orthologs search options">
51 104 <conditional name="ortho_method">
52 <section name="diamond" expanded="true" title="Diamond Options"> 105 <param argument="-m" type="select" label="Method to search seed orthologs">
53 <conditional name="matrix_gapcosts"> 106 <option value="diamond" selected="true">Diamond</option>
54 <param argument="--matrix" type="select" label="Scoring matrix and gap costs"> 107 <option value="mmseqs">MMseqs2</option>
55 <option value="BLOSUM90">BLOSUM90</option>
56 <option value="BLOSUM80">BLOSUM80</option>
57 <option value="BLOSUM62" selected="true">BLOSUM62</option>
58 <option value="BLOSUM50">BLOSUM50</option>
59 <option value="BLOSUM45">BLOSUM45</option>
60 <option value="PAM250">PAM250</option>
61 <option value="PAM70">PAM70</option>
62 <option value="PAM30">PAM30</option>
63 </param> 108 </param>
64 <when value="BLOSUM90"> 109 <when value="diamond">
65 <param name="gap_costs" type="select" label="Gap Costs"> 110 <conditional name="matrix_gapcosts">
66 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> 111 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
67 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> 112 <option value="BLOSUM90">BLOSUM90</option>
68 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> 113 <option value="BLOSUM80">BLOSUM80</option>
69 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> 114 <option value="BLOSUM62" selected="true">BLOSUM62</option>
70 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> 115 <option value="BLOSUM50">BLOSUM50</option>
71 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> 116 <option value="BLOSUM45">BLOSUM45</option>
72 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> 117 <option value="PAM250">PAM250</option>
118 <option value="PAM70">PAM70</option>
119 <option value="PAM30">PAM30</option>
120 </param>
121 <when value="BLOSUM90">
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>
73 </param> 245 </param>
246 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false"
247 label="Run diamond in iterative mode, up to the sensitivity level"/>
248 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false"
249 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/>
74 </when> 250 </when>
75 <when value="BLOSUM80"> 251 <when value="mmseqs">
76 <param name="gap_costs" type="select" label="Gap Costs"> 252 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" />
77 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> 253 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" />
78 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> 254 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" />
79 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
80 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
81 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
82 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
83 </param>
84 </when>
85 <when value="BLOSUM62">
86 <param name="gap_costs" type="select" label="Gap Costs">
87 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
88 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
89 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
90 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
91 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
92 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
93 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
94 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
95 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
96 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
97 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
98 </param>
99 </when>
100 <when value="BLOSUM50">
101 <param name="gap_costs" type="select" label="Gap Costs">
102 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
103 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
104 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
105 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
106 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
107 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
108 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
109 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
110 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
111 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
112 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
113 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
114 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
115 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
116 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
117 </param>
118 </when>
119 <when value="BLOSUM45">
120 <param name="gap_costs" type="select" label="Gap Costs">
121 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
122 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
123 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
124 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
125 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
126 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
127 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
128 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
129 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
130 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
131 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
132 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
133 </param>
134 </when>
135 <when value="PAM250">
136 <param name="gap_costs" type="select" label="Gap Costs">
137 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
138 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
139 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
140 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
141 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
142 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
143 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
144 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
145 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
146 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
147 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</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 </param>
152 </when>
153 <when value="PAM70">
154 <param name="gap_costs" type="select" label="Gap Costs">
155 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
156 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
157 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
158 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
159 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
160 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
161 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
162 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
163 </param>
164 </when>
165 <when value="PAM30">
166 <param name="gap_costs" type="select" label="Gap Costs">
167 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
168 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
169 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
170 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
171 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
172 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
173 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
174 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
175 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
176 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
177 </param>
178 </when> 255 </when>
179 </conditional> 256 </conditional>
180 257
181 <param name="query_cover" type="integer" value="0" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" /> 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" />
182 <param name="subject_cover" type="integer" value="0" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" /> 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" />
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" />
183 </section> 261 </section>
184 262
185 <section name="annotation_options" expanded="false" title="Annotation Options"> 263 <section name="annotation_options" expanded="false" title="Annotation Options">
186 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" /> 264 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
187 <param name="target_orthologs" type="select" label="target orthologs for functional transfer"> 265 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
193 </param> 271 </param>
194 <param name="go_evidence" type="select" 272 <param name="go_evidence" type="select"
195 label="Select the set of GO terms that should be used for annotation"> 273 label="Select the set of GO terms that should be used for annotation">
196 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option> 274 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
197 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option> 275 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
276 <option value="all" selected="true">All (experimental + non-electronic)</option>
198 </param> 277 </param>
199 </section> 278 </section>
200 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options"> 279 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
201 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> 280 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
202 <help> 281 <help>
203 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. 282 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
204 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated. 283 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
205 </help> 284 </help>
206 </param> 285 </param>
207 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold"> 286 <param name="seed_ortholog_score" type="integer" optional="true" min="0" label="Minimum bit score threshold">
208 <help> 287 <help>
209 Min bit score expected when searching for seed eggNOG ortholog. 288 Min bit score expected when searching for seed eggNOG ortholog.
210 Queries not having a significant seed orthologs will not be annotated. 289 Queries not having a significant seed orthologs will not be annotated.
211 </help> 290 </help>
212 </param> 291 </param>
221 </section> 300 </section>
222 </inputs> 301 </inputs>
223 <outputs> 302 <outputs>
224 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs"> 303 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
225 <actions> 304 <actions>
226 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/> 305 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov"/>
227 </actions> 306 </actions>
228 </data> 307 </data>
229 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations"> 308 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
230 <filter>not output_options['no_annot']</filter> 309 <filter>not output_options['no_annot']</filter>
231 <actions> 310 <actions>
232 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_taxonomic_group,predicted_protein_name,GO_terms,EC_number,KEGG_KO,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_free_text_description"/> 311 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
233 </actions> 312 </actions>
234 </data> 313 </data>
235 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs"> 314 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
236 <filter>output_options['report_orthologs']</filter> 315 <filter>output_options['report_orthologs']</filter>
237 <actions> 316 <actions>
238 <action name="column_names" type="metadata" default="query_name,orthologs"/> 317 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
239 </actions> 318 </actions>
240 </data> 319 </data>
241 </outputs> 320 </outputs>
242 <tests> 321 <tests>
243 <test> 322 <test>
266 </section> 345 </section>
267 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> 346 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
268 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> 347 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/>
269 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> 348 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
270 </test> 349 </test>
350 <test>
351 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
352 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
353 <section name="seed_ortho_options">
354 <conditional name="ortho_method">
355 <param name="m" value="diamond" />
356 <param name="sensmode" value="fast" />
357 </conditional>
358 </section>
359 <param name="report_orthologs" value="true"/>
360 <param name="no_file_comments" value="true"/>
361 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
362 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
363 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
364 </test>
365 <!-- not enabled as it requires a specific .db file, hard to minimize -->
366 <!--test>
367 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
368 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
369 <section name="seed_ortho_options">
370 <conditional name="ortho_method">
371 <param name="m" value="mmseqs" />
372 <param name="start_sens" value="4" />
373 </conditional>
374 </section>
375 <param name="report_orthologs" value="true"/>
376 <param name="no_file_comments" value="true"/>
377 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
378 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
379 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
380 </test-->
271 </tests> 381 </tests>
272 <help><![CDATA[ 382 <help><![CDATA[
273 383
274 eggnog-mapper 384 eggnog-mapper
275 ============= 385 =============