Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 4:2667d24b58a0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
author galaxyp
date Wed, 28 Feb 2018 13:20:40 -0500
parents f89f83f30e82
children a5a3bdd0954b
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2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
0
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2 <description>functional sequence annotation by orthology</description>
4
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3 <macros>
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4 <token name="@VERSION@">1.0.3</token>
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5 </macros>
0
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6 <requirements>
4
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7 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
0
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8 </requirements>
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9 <version_command>emapper.py --version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 emapper.py
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12 --data_dir '$eggnog_data.fields.db'
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13 -m $db.mode
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14 $translate
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15 #if ($db.mode == 'hmmer'):
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16 --database=$db.database.fields.db
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17 #if $db.hmm_options.hmm_settings == 'specified':
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18 --hmm_maxhits=$db.hmm_options.hmm_maxhits
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19 --hmm_evalue=$db.hmm_options.hmm_evalue
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20 --hmm_score=$db.hmm_options.hmm_score
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21 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
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22 #if str($db.hmm_options.hmm_qcov):
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23 --hmm_qcov=$db.hmm_options.hmm_qcov
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24 #end if
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25 --Z=$db.hmm_options.Z
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26 #end if
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27 #elif ($db.mode == 'diamond'):
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28 --matrix '$db.matrix_gapcosts.matrix'
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29 $db.matrix_gapcosts.gap_costs
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30 #end if
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31 #if $annotation_options.tax_scope:
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32 --tax_scope=$annotation_options.tax_scope
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33 #end if
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34 #if $annotation_options.target_orthologs:
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35 --target_orthologs=$annotation_options.target_orthologs
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36 #end if
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37 #if $annotation_options.go_evidence:
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38 --go_evidence=$annotation_options.go_evidence
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39 #end if
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40 #if $seed_ortholog_options.seed_ortholog_evalue:
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41 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
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42 #end if
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43 #if str($seed_ortholog_options.seed_ortholog_score):
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44 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
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45 #end if
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46 $output_options.no_file_comments
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47 $output_options.no_annot
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48 $output_options.report_orthologs
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49 --output='results'
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50 -i '${input}'
1
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51 --cpu "\${GALAXY_SLOTS:-4}"
0
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52 ]]></command>
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53 <inputs>
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54 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
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55 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
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56 <options from_data_table="eggnog_mapper">
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57 <filter type="static_value" name="type" value="data" column="2"/>
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58 </options>
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59 </param>
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60 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
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61 label="Are these coding DNA sequences that need to be translated?"/>
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62 <conditional name="db">
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63 <param name="mode" type="select" label="Annotation Type">
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64 <option value="hmmer">HMM</option>
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65 <option value="diamond">DIAMOND</option>
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66 </param>
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67 <when value="hmmer">
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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.">
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69 <options from_data_table="eggnog_mapper">
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70 <filter type="static_value" value="hmmer" column="2"/>
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71 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
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72 </options>
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73 </param>
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74 <conditional name="hmm_options">
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75 <param name="hmm_settings" type="select" label="HMM Search Options">
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76 <option value="default">Use defaults</option>
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77 <option value="specified">Set HMM Search Options</option>
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78 </param>
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79 <when value="default"/>
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80 <when value="specified">
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81 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
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82 <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" />
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83 <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
84 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
85 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
86 <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" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
87 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
88 </conditional>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
89 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
90 <when value="diamond">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
91 <!-- db.database is used in diamond mode only to name outputs -->
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
92 <param name="database" type="hidden" value="diamond"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
93 <conditional name="matrix_gapcosts">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
94 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
95 <option value="BLOSUM90">BLOSUM90</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
96 <option value="BLOSUM80">BLOSUM80</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
97 <option value="BLOSUM62" selected="true">BLOSUM62</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
98 <option value="BLOSUM50">BLOSUM50</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
99 <option value="BLOSUM45">BLOSUM45</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
100 <option value="PAM250">PAM250</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
101 <option value="PAM70">PAM70</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
102 <option value="PAM30">PAM30</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
103 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
104 <when value="BLOSUM90">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
105 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
106 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
107 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
108 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
109 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
110 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
111 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
112 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
113 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
114 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
115 <when value="BLOSUM80">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
116 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
117 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
118 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
119 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
120 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
121 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
122 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
123 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
124 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
125 <when value="BLOSUM62">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
126 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
127 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
128 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
129 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
130 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
131 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
132 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
133 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
134 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
135 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
136 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
137 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
138 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
139 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
140 <when value="BLOSUM50">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
141 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
142 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
143 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
144 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
145 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
146 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
147 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
148 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
149 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
150 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
151 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
152 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
153 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
154 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
155 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
156 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
157 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
158 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
159 <when value="BLOSUM45">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
160 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
161 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
162 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
163 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
164 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
165 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
166 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
167 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
168 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
169 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
170 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
171 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
172 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
173 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
174 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
175 <when value="PAM250">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
176 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
177 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
178 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
179 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
180 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
181 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
182 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
183 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
184 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
185 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
186 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
187 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
188 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
189 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
190 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
191 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
192 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
193 <when value="PAM70">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
194 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
195 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
196 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
197 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
198 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
199 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
200 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
201 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
202 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
203 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
204 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
205 <when value="PAM30">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
206 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
207 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
208 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
209 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
210 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
211 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
212 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
213 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
214 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
215 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
216 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
217 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
218 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
219 </conditional>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
220 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
221 </conditional>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
222 <section name="annotation_options" expanded="false" title="Annotation Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
223 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
224 <option value="NOG">All organisms (NOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
225 <option value="aciNOG">Acidobacteria (aciNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
226 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
227 <option value="acoNOG">Aconoidasida (acoNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
228 <option value="actNOG">Actinobacteria (actNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
229 <option value="agaNOG">Agaricales (agaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
230 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
231 <option value="apiNOG">Apicomplexa (apiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
232 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
233 <option value="aquNOG">Aquificae (aquNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
234 <option value="arNOG">Archaea (arNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
235 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
236 <option value="artNOG">Arthropoda (artNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
237 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
238 <option value="ascNOG">Ascomycota (ascNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
239 <option value="aveNOG">Aves (aveNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
240 <option value="bacNOG">Bacilli (bacNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
241 <option value="bactNOG">Bacteria (bactNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
242 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
243 <option value="basNOG">Basidiomycota (basNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
244 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
245 <option value="biNOG">Bilateria (biNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
246 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
247 <option value="braNOG">Brassicales (braNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
248 <option value="carNOG">Carnivora (carNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
249 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
250 <option value="chlNOG">Chlorobi (chlNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
251 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
252 <option value="chloNOG">Chloroflexi (chloNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
253 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
254 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
255 <option value="chorNOG">Chordata (chorNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
256 <option value="chrNOG">Chromadorea (chrNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
257 <option value="cloNOG">Clostridia (cloNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
258 <option value="cocNOG">Coccidia (cocNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
259 <option value="creNOG">Crenarchaeota (creNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
260 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
261 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
262 <option value="cytNOG">Cytophagia (cytNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
263 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
264 <option value="defNOG">Deferribacteres (defNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
265 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
266 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
267 <option value="delNOG">delta/epsilon (delNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
268 <option value="dipNOG">Diptera (dipNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
269 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
270 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
271 <option value="droNOG">Drosophilidae (droNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
272 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
273 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
274 <option value="euNOG">Eukaryotes (euNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
275 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
276 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
277 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
278 <option value="fiNOG">Fishes (fiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
279 <option value="firmNOG">Firmicutes (firmNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
280 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
281 <option value="fuNOG">Fungi (fuNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
282 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
283 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
284 <option value="haeNOG">Haemosporida (haeNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
285 <option value="halNOG">Halobacteria (halNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
286 <option value="homNOG">Hominidae (homNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
287 <option value="hymNOG">Hymenoptera (hymNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
288 <option value="hypNOG">Hypocreales (hypNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
289 <option value="inNOG">Insects (inNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
290 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
291 <option value="lepNOG">Lepidoptera (lepNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
292 <option value="lilNOG">Liliopsida (lilNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
293 <option value="maNOG">Mammals (maNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
294 <option value="magNOG">Magnaporthales (magNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
295 <option value="meNOG">Animals (meNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
296 <option value="metNOG">Methanobacteria (metNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
297 <option value="methNOG">Methanococci (methNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
298 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
299 <option value="necNOG">Nectriaceae (necNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
300 <option value="negNOG">Negativicutes (negNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
301 <option value="nemNOG">Nematodes (nemNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
302 <option value="onyNOG">Onygenales (onyNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
303 <option value="opiNOG">Opisthokonts (opiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
304 <option value="perNOG">Peronosporales (perNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
305 <option value="plaNOG">Planctomycetes (plaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
306 <option value="pleNOG">Pleosporales (pleNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
307 <option value="poaNOG">Poales (poaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
308 <option value="prNOG">Primates (prNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
309 <option value="proNOG">Proteobacteria (proNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
310 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
311 <option value="roNOG">Rodents (roNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
312 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
313 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
314 <option value="sorNOG">Sordariales (sorNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
315 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
316 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
317 <option value="spiNOG">Spirochaetes (spiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
318 <option value="spriNOG">Supraprimates (spriNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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319 <option value="strNOG">Streptophyta (strNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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320 <option value="synNOG">Synergistetes (synNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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321 <option value="tenNOG">Tenericutes (tenNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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322 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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323 <option value="theNOG">Thermoplasmata (theNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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324 <option value="therNOG">Thermotogae (therNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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325 <option value="thermNOG">Thermococci (thermNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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326 <option value="treNOG">Tremellales (treNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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327 <option value="veNOG">Vertebrates (veNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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328 <option value="verNOG">Verrucomicrobia (verNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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329 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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330 <option value="virNOG">Viridiplantae (virNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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331 </param>
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332 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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333 <option value="one2one">one2one</option>
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334 <option value="many2one">many2one</option>
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335 <option value="one2many">one2many</option>
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336 <option value="many2many">many2many</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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337 <option value="all" selected="true">all</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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338 </param>
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339 <param name="go_evidence" type="select"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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340 label="Select the set of GO terms that should be used for annotation">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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341 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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342 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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343 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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344 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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345 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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346 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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347 <help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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348 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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349 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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350 </help>
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351 </param>
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352 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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353 <help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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354 Min bit score expected when searching for seed eggNOG ortholog.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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355 Queries not having a significant seed orthologs will not be annotated.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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356 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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357 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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358 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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359 <section name="output_options" expanded="false" title="Output Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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360 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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361 label="Exclude header lines and stats from output files"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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362 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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363 label="Skip functional annotation, reporting only hits"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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364 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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365 label="Output a file with the list of orthologs for each hits"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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366 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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367 </inputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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368 <outputs>
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369 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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370 <actions>
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371 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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372 </actions>
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373 </data>
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374 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
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375 <filter>not output_options['no_annot']</filter>
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376 <actions>
3
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377 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_KO,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_HMM_model_annotation"/>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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378 </actions>
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379 </data>
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380 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits">
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381 <filter>db['mode'] == 'hmmer'</filter>
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382 <actions>
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383 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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384 </actions>
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385 </data>
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386 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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387 <filter>output_options['report_orthologs']</filter>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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388 <actions>
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389 <action name="column_names" type="metadata" default="query_name,orthologs"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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390 </actions>
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391 </data>
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392 </outputs>
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393 <tests>
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394 <test>
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395 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
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396 <param name="database" value="ENOG411CB2I"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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397 <param name="mode" value="hmmer"/>
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398 <param name="test" value="true"/>
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399 <param name="eggnog_data" value="eggNOG_4.5"/>
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400 <param name="no_annot" value="true"/>
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401 <param name="no_file_comments" value="true"/>
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402 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
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403 </test>
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404 <test>
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405 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
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406 <param name="eggnog_data" value="eggNOG_4.5"/> <!-- not passed in test, but required for test to work -->
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407 <param name="no_annot" value="true"/>
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408 <param name="mode" value="diamond"/>
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409 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
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410 </test>
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411 </tests>
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412 <help><![CDATA[
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413
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414 eggnog-mapper
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415 =============
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416 Overview
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417 --------
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418
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419 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
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420 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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421 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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422 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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423
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424 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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425
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426 Options
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427 -------
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428
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429 ``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_.
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430 HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences.
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431
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432
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433 Outputs
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434 -------
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435
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436 **hmm_hits**
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437
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438 For each query sequence, a list of significant
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439 hits to eggNOG Orthologous Groups (OGs) is reported.
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440 Each line in the file represents a hit, where evalue, bit-score,
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441 query-coverage and the sequence coordinates of the match are reported.
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442 If multiple hits exist for a given query, results are sorted by e-value.
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443 Only returned when using HMMER mode.
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444
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445 **seed_orthologs**
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446
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447 each line in the file provides the best match of each query within the best Orthologous Group (OG)
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448 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
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449 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
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450 If using the diamond search mode, seed orthologs are directly
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451 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
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452
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453 **annotations**
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454
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455 This file provides final annotations of each query. Tab-delimited columns in the file are:
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456
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457 - ``query_name``: query sequence name
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458 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
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459 - ``seed_ortholog_evalue``: best protein match (e-value)
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460 - ``seed_ortholog_score``: best protein match (bit-score)
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461 - ``predicted_gene_name``: Predicted gene name for query sequences
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462 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
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463 - ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
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464 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
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465 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
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466 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
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467 - ``COG functional categories``: COG functional category inferred from best matching OG
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468 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
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469
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470 ]]></help>
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471 <citations>
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472 <citation type="doi">10.1093/nar/gkv1248</citation>
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473 </citations>
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474 </tool>