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comparison eggnog_mapper.xml @ 6:3cb37af59360 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Sat, 05 Sep 2020 07:21:28 +0000
parents a5a3bdd0954b
children 4e4c6329f6cd
comparison
equal deleted inserted replaced
5:a5a3bdd0954b 6:3cb37af59360
1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1"> 1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
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 emapper.py 9 emapper.py
10 --data_dir '$eggnog_data.fields.path' 10 --data_dir '$eggnog_data.fields.path'
11 -m $db.mode 11 -m diamond
12 $translate 12 $translate
13 #if ($db.mode == 'hmmer'): 13
14 #if $db.database.fields.path: 14 ## Diamond option
15 --database=$db.database.fields.path 15 --matrix '$diamond.matrix_gapcosts.matrix'
16 #else 16 $diamond.matrix_gapcosts.gap_costs
17 --database=$db.database 17 --query-cover $diamond.query_cover
18 #end if 18 --subject-cover $diamond.subject_cover
19 #if $db.hmm_options.hmm_settings == 'specified': 19
20 --hmm_maxhits=$db.hmm_options.hmm_maxhits
21 --hmm_evalue=$db.hmm_options.hmm_evalue
22 --hmm_score=$db.hmm_options.hmm_score
23 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
24 #if str($db.hmm_options.hmm_qcov):
25 --hmm_qcov=$db.hmm_options.hmm_qcov
26 #end if
27 --Z=$db.hmm_options.Z
28 #end if
29 #elif ($db.mode == 'diamond'):
30 --matrix '$db.matrix_gapcosts.matrix'
31 $db.matrix_gapcosts.gap_costs
32 #end if
33 #if $annotation_options.tax_scope: 20 #if $annotation_options.tax_scope:
34 --tax_scope=$annotation_options.tax_scope 21 --tax_scope=$annotation_options.tax_scope
35 #end if 22 #end if
36 #if $annotation_options.target_orthologs: 23 #if $annotation_options.target_orthologs:
37 --target_orthologs=$annotation_options.target_orthologs 24 --target_orthologs=$annotation_options.target_orthologs
38 #end if 25 #end if
39 #if $annotation_options.go_evidence: 26 #if $annotation_options.go_evidence:
40 --go_evidence=$annotation_options.go_evidence 27 --go_evidence=$annotation_options.go_evidence
41 #end if 28 #end if
42 #if $seed_ortholog_options.seed_ortholog_evalue: 29 #if $seed_ortholog_options.seed_ortholog_evalue:
43 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue 30 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
44 #end if 31 #end if
45 #if str($seed_ortholog_options.seed_ortholog_score): 32 #if str($seed_ortholog_options.seed_ortholog_score):
46 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score 33 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
47 #end if 34 #end if
48 $output_options.no_file_comments 35 $output_options.no_file_comments
49 $output_options.no_annot 36 $output_options.no_annot
50 $output_options.report_orthologs 37 $output_options.report_orthologs
51 --output='results' 38 --output='results'
52 -i '${input}' 39 -i '${input}'
53 --cpu "\${GALAXY_SLOTS:-4}" 40 --cpu "\${GALAXY_SLOTS:-4}"
54 ]]></command> 41 ]]></command>
55 <inputs> 42 <inputs>
56 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> 43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
57 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> 44 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
58 <options from_data_table="eggnog_mapper_db"/> 45 <options from_data_table="eggnog_mapper_db"/>
59 </param> 46 </param>
60 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" 47 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
61 label="Are these coding DNA sequences that need to be translated?"/> 48 label="Are these coding DNA sequences that need to be translated?"/>
62 <conditional name="db"> 49
63 <param name="mode" type="select" label="Annotation Type"> 50 <section name="diamond" expanded="true" title="Diamond Options">
64 <option value="hmmer">HMM</option> 51 <conditional name="matrix_gapcosts">
65 <option value="diamond">DIAMOND</option> 52 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
53 <option value="BLOSUM90">BLOSUM90</option>
54 <option value="BLOSUM80">BLOSUM80</option>
55 <option value="BLOSUM62" selected="true">BLOSUM62</option>
56 <option value="BLOSUM50">BLOSUM50</option>
57 <option value="BLOSUM45">BLOSUM45</option>
58 <option value="PAM250">PAM250</option>
59 <option value="PAM70">PAM70</option>
60 <option value="PAM30">PAM30</option>
66 </param> 61 </param>
67 <when value="hmmer"> 62 <when value="BLOSUM90">
68 <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed."> 63 <param name="gap_costs" type="select" label="Gap Costs">
69 <options from_data_table="eggnog_mapper_hmm_dbs"> 64 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
70 <!-- 65 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
71 <filter type="param_value" ref="eggnog_data" column="1" /> 66 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
72 <filter type="unique_value" column="3" /> 67 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
73 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." /> 68 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
74 --> 69 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
75 </options> 70 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
76 </param> 71 </param>
77 <conditional name="hmm_options"> 72 </when>
78 <param name="hmm_settings" type="select" label="HMM Search Options"> 73 <when value="BLOSUM80">
79 <option value="default">Use defaults</option> 74 <param name="gap_costs" type="select" label="Gap Costs">
80 <option value="specified">Set HMM Search Options</option> 75 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
81 </param> 76 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
82 <when value="default"/> 77 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
83 <when value="specified"> 78 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
84 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/> 79 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
85 <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" /> 80 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
86 <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" /> 81 </param>
87 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" /> 82 </when>
88 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" /> 83 <when value="BLOSUM62">
89 <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" /> 84 <param name="gap_costs" type="select" label="Gap Costs">
90 </when> 85 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
91 </conditional> 86 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
92 </when> 87 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
93 <when value="diamond"> 88 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
94 <!-- db.database is used in diamond mode only to name outputs --> 89 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
95 <param name="database" type="hidden" value="diamond"/> 90 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
96 <conditional name="matrix_gapcosts"> 91 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
97 <param argument="--matrix" type="select" label="Scoring matrix and gap costs"> 92 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
98 <option value="BLOSUM90">BLOSUM90</option> 93 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
99 <option value="BLOSUM80">BLOSUM80</option> 94 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
100 <option value="BLOSUM62" selected="true">BLOSUM62</option> 95 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
101 <option value="BLOSUM50">BLOSUM50</option> 96 </param>
102 <option value="BLOSUM45">BLOSUM45</option> 97 </when>
103 <option value="PAM250">PAM250</option> 98 <when value="BLOSUM50">
104 <option value="PAM70">PAM70</option> 99 <param name="gap_costs" type="select" label="Gap Costs">
105 <option value="PAM30">PAM30</option> 100 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
106 </param> 101 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
107 <when value="BLOSUM90"> 102 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
108 <param name="gap_costs" type="select" label="Gap Costs"> 103 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
109 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> 104 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
110 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> 105 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
111 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> 106 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
112 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> 107 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
113 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> 108 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
114 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> 109 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
115 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> 110 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
116 </param> 111 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
117 </when> 112 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
118 <when value="BLOSUM80"> 113 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
119 <param name="gap_costs" type="select" label="Gap Costs"> 114 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
120 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> 115 </param>
121 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> 116 </when>
122 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> 117 <when value="BLOSUM45">
123 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> 118 <param name="gap_costs" type="select" label="Gap Costs">
124 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> 119 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
125 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> 120 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
126 </param> 121 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
127 </when> 122 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
128 <when value="BLOSUM62"> 123 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
129 <param name="gap_costs" type="select" label="Gap Costs"> 124 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
130 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> 125 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
131 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option> 126 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
132 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> 127 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
133 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> 128 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
134 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> 129 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
135 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> 130 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
136 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option> 131 </param>
137 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option> 132 </when>
138 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option> 133 <when value="PAM250">
139 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> 134 <param name="gap_costs" type="select" label="Gap Costs">
140 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> 135 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
141 </param> 136 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
142 </when> 137 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
143 <when value="BLOSUM50"> 138 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
144 <param name="gap_costs" type="select" label="Gap Costs"> 139 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
145 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> 140 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
146 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> 141 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
147 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> 142 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
148 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> 143 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
149 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option> 144 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
150 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> 145 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
151 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> 146 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
152 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> 147 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
153 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option> 148 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
154 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> 149 </param>
155 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> 150 </when>
156 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> 151 <when value="PAM70">
157 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> 152 <param name="gap_costs" type="select" label="Gap Costs">
158 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> 153 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
159 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option> 154 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
160 </param> 155 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
161 </when> 156 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
162 <when value="BLOSUM45"> 157 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
163 <param name="gap_costs" type="select" label="Gap Costs"> 158 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
164 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> 159 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
165 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> 160 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
166 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> 161 </param>
167 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> 162 </when>
168 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option> 163 <when value="PAM30">
169 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> 164 <param name="gap_costs" type="select" label="Gap Costs">
170 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> 165 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
171 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> 166 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
172 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> 167 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
173 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> 168 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
174 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> 169 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
175 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> 170 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
176 </param> 171 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
177 </when> 172 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
178 <when value="PAM250"> 173 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
179 <param name="gap_costs" type="select" label="Gap Costs"> 174 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
180 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> 175 </param>
181 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
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 17 --gapextend 2">Existence: 17 Extension: 2</option>
185 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
186 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
187 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
188 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
189 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
190 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
191 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
192 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
193 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
194 </param>
195 </when>
196 <when value="PAM70">
197 <param name="gap_costs" type="select" label="Gap Costs">
198 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
199 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
200 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
201 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
202 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
203 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
204 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
205 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
206 </param>
207 </when>
208 <when value="PAM30">
209 <param name="gap_costs" type="select" label="Gap Costs">
210 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
211 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
212 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
213 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
214 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
215 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
216 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
217 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
218 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
219 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
220 </param>
221 </when>
222 </conditional>
223 </when> 176 </when>
224 </conditional> 177 </conditional>
178
179 <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" />
180 <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" />
181 </section>
182
225 <section name="annotation_options" expanded="false" title="Annotation Options"> 183 <section name="annotation_options" expanded="false" title="Annotation Options">
226 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope"> 184 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
227 <option value="NOG">All organisms (NOG)</option>
228 <option value="aciNOG">Acidobacteria (aciNOG)</option>
229 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
230 <option value="acoNOG">Aconoidasida (acoNOG)</option>
231 <option value="actNOG">Actinobacteria (actNOG)</option>
232 <option value="agaNOG">Agaricales (agaNOG)</option>
233 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
234 <option value="apiNOG">Apicomplexa (apiNOG)</option>
235 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
236 <option value="aquNOG">Aquificae (aquNOG)</option>
237 <option value="arNOG">Archaea (arNOG)</option>
238 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
239 <option value="artNOG">Arthropoda (artNOG)</option>
240 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
241 <option value="ascNOG">Ascomycota (ascNOG)</option>
242 <option value="aveNOG">Aves (aveNOG)</option>
243 <option value="bacNOG">Bacilli (bacNOG)</option>
244 <option value="bactNOG">Bacteria (bactNOG)</option>
245 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
246 <option value="basNOG">Basidiomycota (basNOG)</option>
247 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
248 <option value="biNOG">Bilateria (biNOG)</option>
249 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
250 <option value="braNOG">Brassicales (braNOG)</option>
251 <option value="carNOG">Carnivora (carNOG)</option>
252 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
253 <option value="chlNOG">Chlorobi (chlNOG)</option>
254 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
255 <option value="chloNOG">Chloroflexi (chloNOG)</option>
256 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
257 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
258 <option value="chorNOG">Chordata (chorNOG)</option>
259 <option value="chrNOG">Chromadorea (chrNOG)</option>
260 <option value="cloNOG">Clostridia (cloNOG)</option>
261 <option value="cocNOG">Coccidia (cocNOG)</option>
262 <option value="creNOG">Crenarchaeota (creNOG)</option>
263 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
264 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
265 <option value="cytNOG">Cytophagia (cytNOG)</option>
266 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
267 <option value="defNOG">Deferribacteres (defNOG)</option>
268 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
269 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
270 <option value="delNOG">delta/epsilon (delNOG)</option>
271 <option value="dipNOG">Diptera (dipNOG)</option>
272 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
273 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
274 <option value="droNOG">Drosophilidae (droNOG)</option>
275 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
276 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
277 <option value="euNOG">Eukaryotes (euNOG)</option>
278 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
279 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
280 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
281 <option value="fiNOG">Fishes (fiNOG)</option>
282 <option value="firmNOG">Firmicutes (firmNOG)</option>
283 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
284 <option value="fuNOG">Fungi (fuNOG)</option>
285 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
286 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
287 <option value="haeNOG">Haemosporida (haeNOG)</option>
288 <option value="halNOG">Halobacteria (halNOG)</option>
289 <option value="homNOG">Hominidae (homNOG)</option>
290 <option value="hymNOG">Hymenoptera (hymNOG)</option>
291 <option value="hypNOG">Hypocreales (hypNOG)</option>
292 <option value="inNOG">Insects (inNOG)</option>
293 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
294 <option value="lepNOG">Lepidoptera (lepNOG)</option>
295 <option value="lilNOG">Liliopsida (lilNOG)</option>
296 <option value="maNOG">Mammals (maNOG)</option>
297 <option value="magNOG">Magnaporthales (magNOG)</option>
298 <option value="meNOG">Animals (meNOG)</option>
299 <option value="metNOG">Methanobacteria (metNOG)</option>
300 <option value="methNOG">Methanococci (methNOG)</option>
301 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
302 <option value="necNOG">Nectriaceae (necNOG)</option>
303 <option value="negNOG">Negativicutes (negNOG)</option>
304 <option value="nemNOG">Nematodes (nemNOG)</option>
305 <option value="onyNOG">Onygenales (onyNOG)</option>
306 <option value="opiNOG">Opisthokonts (opiNOG)</option>
307 <option value="perNOG">Peronosporales (perNOG)</option>
308 <option value="plaNOG">Planctomycetes (plaNOG)</option>
309 <option value="pleNOG">Pleosporales (pleNOG)</option>
310 <option value="poaNOG">Poales (poaNOG)</option>
311 <option value="prNOG">Primates (prNOG)</option>
312 <option value="proNOG">Proteobacteria (proNOG)</option>
313 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
314 <option value="roNOG">Rodents (roNOG)</option>
315 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
316 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
317 <option value="sorNOG">Sordariales (sorNOG)</option>
318 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
319 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
320 <option value="spiNOG">Spirochaetes (spiNOG)</option>
321 <option value="spriNOG">Supraprimates (spriNOG)</option>
322 <option value="strNOG">Streptophyta (strNOG)</option>
323 <option value="synNOG">Synergistetes (synNOG)</option>
324 <option value="tenNOG">Tenericutes (tenNOG)</option>
325 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
326 <option value="theNOG">Thermoplasmata (theNOG)</option>
327 <option value="therNOG">Thermotogae (therNOG)</option>
328 <option value="thermNOG">Thermococci (thermNOG)</option>
329 <option value="treNOG">Tremellales (treNOG)</option>
330 <option value="veNOG">Vertebrates (veNOG)</option>
331 <option value="verNOG">Verrucomicrobia (verNOG)</option>
332 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
333 <option value="virNOG">Viridiplantae (virNOG)</option>
334 </param>
335 <param name="target_orthologs" type="select" label="target orthologs for functional transfer"> 185 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
336 <option value="one2one">one2one</option> 186 <option value="one2one">one2one</option>
337 <option value="many2one">many2one</option> 187 <option value="many2one">many2one</option>
338 <option value="one2many">one2many</option> 188 <option value="one2many">one2many</option>
339 <option value="many2many">many2many</option> 189 <option value="many2many">many2many</option>
346 </param> 196 </param>
347 </section> 197 </section>
348 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options"> 198 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
349 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> 199 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
350 <help> 200 <help>
351 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. 201 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
352 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated. 202 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
353 </help> 203 </help>
354 </param> 204 </param>
355 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold"> 205 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
356 <help> 206 <help>
357 Min bit score expected when searching for seed eggNOG ortholog. 207 Min bit score expected when searching for seed eggNOG ortholog.
358 Queries not having a significant seed orthologs will not be annotated. 208 Queries not having a significant seed orthologs will not be annotated.
359 </help> 209 </help>
360 </param> 210 </param>
361 </section> 211 </section>
362 <section name="output_options" expanded="false" title="Output Options"> 212 <section name="output_options" expanded="false" title="Output Options">
367 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" 217 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
368 label="Output a file with the list of orthologs for each hits"/> 218 label="Output a file with the list of orthologs for each hits"/>
369 </section> 219 </section>
370 </inputs> 220 </inputs>
371 <outputs> 221 <outputs>
372 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs"> 222 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
373 <actions> 223 <actions>
374 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/> 224 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
375 </actions> 225 </actions>
376 </data> 226 </data>
377 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations"> 227 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
378 <filter>not output_options['no_annot']</filter> 228 <filter>not output_options['no_annot']</filter>
379 <actions> 229 <actions>
380 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_KO,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_HMM_model_annotation"/> 230 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_taxonomic_group,predicted_protein_name,GO_terms,EC_number,KEGG_KO,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_free_text_description"/>
381 </actions> 231 </actions>
382 </data> 232 </data>
383 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits"> 233 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
384 <filter>db['mode'] == 'hmmer'</filter>
385 <actions>
386 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
387 </actions>
388 </data>
389 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
390 <filter>output_options['report_orthologs']</filter> 234 <filter>output_options['report_orthologs']</filter>
391 <actions> 235 <actions>
392 <action name="column_names" type="metadata" default="query_name,orthologs"/> 236 <action name="column_names" type="metadata" default="query_name,orthologs"/>
393 </actions> 237 </actions>
394 </data> 238 </data>
395 </outputs> 239 </outputs>
396 <tests> 240 <tests>
397 <test> 241 <test>
398 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> 242 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
399 <param name="database" value="ENOG411CB2I"/> 243 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
400 <param name="mode" value="hmmer"/>
401 <!--
402 <param name="test" value="true"/>
403 -->
404 <param name="eggnog_data" value="4.5"/>
405 <param name="no_annot" value="true"/> 244 <param name="no_annot" value="true"/>
406 <param name="no_file_comments" value="true"/> 245 <param name="no_file_comments" value="true"/>
407 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/> 246 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
408 </test> 247 </test>
409 <test> 248 <test>
410 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> 249 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
411 <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work --> 250 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
412 <param name="no_annot" value="true"/> 251 <param name="report_orthologs" value="true"/>
413 <param name="mode" value="diamond"/> 252 <param name="no_file_comments" value="true"/>
414 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> 253 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
254 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular"/>
255 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
256 </test>
257 <test>
258 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
259 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
260 <param name="report_orthologs" value="true"/>
261 <param name="no_file_comments" value="true"/>
262 <section name="annotation_options">
263 <param name="tax_scope" value="651137" />
264 </section>
265 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular"/>
266 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular"/>
267 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
415 </test> 268 </test>
416 </tests> 269 </tests>
417 <help><![CDATA[ 270 <help><![CDATA[
418 271
419 eggnog-mapper 272 eggnog-mapper
420 ============= 273 =============
421 Overview 274 Overview
422 -------- 275 --------
423 276
424 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. 277 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
425 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. 278 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
426 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, 279 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
427 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence). 280 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
428 281
429 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_. 282 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
430
431 Options
432 -------
433
434 ``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_.
435 HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences.
436
437 283
438 Outputs 284 Outputs
439 ------- 285 -------
440 286
441 **hmm_hits**
442
443 For each query sequence, a list of significant
444 hits to eggNOG Orthologous Groups (OGs) is reported.
445 Each line in the file represents a hit, where evalue, bit-score,
446 query-coverage and the sequence coordinates of the match are reported.
447 If multiple hits exist for a given query, results are sorted by e-value.
448 Only returned when using HMMER mode.
449
450 **seed_orthologs** 287 **seed_orthologs**
451 288
452 each line in the file provides the best match of each query within the best Orthologous Group (OG) 289 each line in the file provides the best match of each query within the best Orthologous Group (OG)
453 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. 290 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
454 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. 291 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
455 If using the diamond search mode, seed orthologs are directly 292 If using the diamond search mode, seed orthologs are directly
456 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space. 293 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
457 294
458 **annotations** 295 **annotations**
459 296
460 This file provides final annotations of each query. Tab-delimited columns in the file are: 297 This file provides final annotations of each query. Tab-delimited columns in the file are:
461 298
462 - ``query_name``: query sequence name 299 - ``query_name``: query sequence name
463 - ``seed_eggNOG_ortholog``: best protein match in eggNOG 300 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
464 - ``seed_ortholog_evalue``: best protein match (e-value) 301 - ``seed_ortholog_evalue``: best protein match (e-value)
465 - ``seed_ortholog_score``: best protein match (bit-score) 302 - ``seed_ortholog_score``: best protein match (bit-score)
466 - ``predicted_gene_name``: Predicted gene name for query sequences 303 - ``predicted_taxonomic_group``
304 - ``predicted_protein_name``: Predicted protein name for query sequences
467 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms 305 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
468 - ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways 306 - ``EC_number``
307 - ``KEGG_KO``
308 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
309 - ``KEGG_Module``
310 - ``KEGG_Reaction``
311 - ``KEGG_rclass``
312 - ``BRITE``
313 - ``KEGG_TC``
314 - ``CAZy``
315 - ``BiGG_Reactions``
469 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence 316 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
470 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups 317 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
471 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode) 318 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
472 - ``COG functional categories``: COG functional category inferred from best matching OG 319 - ``COG_functional_categories``: COG functional category inferred from best matching OG
473 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG 320 - ``eggNOG_free_text_description``
474 321
475 ]]></help> 322 ]]></help>
476 <expand macro="citations"/> 323 <expand macro="citations"/>
477 </tool> 324 </tool>