Mercurial > repos > jjohnson > eggnog_mapper

annotate eggnog_mapper.xml @ 8:c2d4738c3282 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 288c3043b10594647e9f6e5de56bf98a38779f75-dirty
author jjohnson
date Fri, 08 Nov 2019 14:40:14 -0500
parents a093b9061498
children
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">
0
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2 <description>functional sequence annotation by orthology</description>
2
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3 <macros>
5
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4 <import>eggnog_macros.xml</import>
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5 </macros>
5
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 emapper.py
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10 --data_dir '$eggnog_data.fields.path'
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11 -m $db.mode
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12 $translate
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13 #if ($db.mode == 'hmmer'):
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14 #if $db.database.fields.path:
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15 --database=$db.database.fields.path
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16 #else
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17 --database=$db.database
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18 #end if
0
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19 #if $db.hmm_options.hmm_settings == 'specified':
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20 --hmm_maxhits=$db.hmm_options.hmm_maxhits
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21 --hmm_evalue=$db.hmm_options.hmm_evalue
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22 --hmm_score=$db.hmm_options.hmm_score
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23 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
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24 #if str($db.hmm_options.hmm_qcov):
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25 --hmm_qcov=$db.hmm_options.hmm_qcov
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26 #end if
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27 --Z=$db.hmm_options.Z
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28 #end if
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29 #elif ($db.mode == 'diamond'):
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30 --matrix '$db.matrix_gapcosts.matrix'
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31 $db.matrix_gapcosts.gap_costs
0
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32 #end if
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33 #if $annotation_options.tax_scope:
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34 --tax_scope=$annotation_options.tax_scope
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35 #end if
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36 #if $annotation_options.target_orthologs:
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37 --target_orthologs=$annotation_options.target_orthologs
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38 #end if
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39 #if $annotation_options.go_evidence:
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40 --go_evidence=$annotation_options.go_evidence
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41 #end if
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42 #if $seed_ortholog_options.seed_ortholog_evalue:
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43 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
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44 #end if
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45 #if str($seed_ortholog_options.seed_ortholog_score):
0
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46 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
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47 #end if
2
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48 $output_options.no_file_comments
0
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49 $output_options.no_annot
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50 $output_options.report_orthologs
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51 --output='results'
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52 -i '${input}'
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53 --cpu "\${GALAXY_SLOTS:-4}"
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54 ]]></command>
2
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55 <inputs>
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56 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
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57 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
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58 <options from_data_table="eggnog_mapper_db"/>
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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>
2
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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_hmm_dbs">
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70 <!--
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71 <filter type="param_value" ref="eggnog_data" column="1" />
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72 <filter type="unique_value" column="3" />
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73 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
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74 -->
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75 </options>
0
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76 </param>
2
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77 <conditional name="hmm_options">
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78 <param name="hmm_settings" type="select" label="HMM Search Options">
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79 <option value="default">Use defaults</option>
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80 <option value="specified">Set HMM Search Options</option>
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81 </param>
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82 <when value="default"/>
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83 <when value="specified">
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84 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
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85 <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" />
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86 <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
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87 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" />
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88 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
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89 <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" />
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90 </when>
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91 </conditional>
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92 </when>
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93 <when value="diamond">
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94 <!-- db.database is used in diamond mode only to name outputs -->
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95 <param name="database" type="hidden" value="diamond"/>
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96 <conditional name="matrix_gapcosts">
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97 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
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98 <option value="BLOSUM90">BLOSUM90</option>
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99 <option value="BLOSUM80">BLOSUM80</option>
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100 <option value="BLOSUM62" selected="true">BLOSUM62</option>
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101 <option value="BLOSUM50">BLOSUM50</option>
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102 <option value="BLOSUM45">BLOSUM45</option>
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103 <option value="PAM250">PAM250</option>
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104 <option value="PAM70">PAM70</option>
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105 <option value="PAM30">PAM30</option>
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106 </param>
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107 <when value="BLOSUM90">
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108 <param name="gap_costs" type="select" label="Gap Costs">
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109 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
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110 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
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111 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
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112 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
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113 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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114 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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115 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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116 </param>
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117 </when>
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118 <when value="BLOSUM80">
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119 <param name="gap_costs" type="select" label="Gap Costs">
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120 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
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parents: 1
diff changeset
121 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
122 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
123 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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parents: 1
diff changeset
124 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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parents: 1
diff changeset
125 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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diff changeset
126 </param>
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diff changeset
127 </when>
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diff changeset
128 <when value="BLOSUM62">
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129 <param name="gap_costs" type="select" label="Gap Costs">
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parents: 1
diff changeset
130 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
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parents: 1
diff changeset
131 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
132 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
133 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
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parents: 1
diff changeset
134 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
135 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
136 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
137 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
138 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
139 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
140 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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diff changeset
141 </param>
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142 </when>
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diff changeset
143 <when value="BLOSUM50">
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parents: 1
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144 <param name="gap_costs" type="select" label="Gap Costs">
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parents: 1
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145 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
146 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
147 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
148 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
149 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
150 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
151 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
152 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
153 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
154 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
155 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
156 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
157 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
158 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
159 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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diff changeset
160 </param>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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diff changeset
161 </when>
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parents: 1
diff changeset
162 <when value="BLOSUM45">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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parents: 1
diff changeset
163 <param name="gap_costs" type="select" label="Gap Costs">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
164 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
165 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
166 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
167 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
168 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
169 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
170 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
171 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
172 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
173 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
174 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
175 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
176 </param>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
177 </when>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
178 <when value="PAM250">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
179 <param name="gap_costs" type="select" label="Gap Costs">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
180 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
181 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
182 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
183 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
184 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
185 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
186 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
187 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
188 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
189 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
190 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
191 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
192 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
193 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
194 </param>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
195 </when>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
196 <when value="PAM70">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
197 <param name="gap_costs" type="select" label="Gap Costs">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
198 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
199 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
200 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
201 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
202 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
203 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
204 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
205 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
206 </param>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
207 </when>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
208 <when value="PAM30">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
209 <param name="gap_costs" type="select" label="Gap Costs">
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
210 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
211 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
212 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
213 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
214 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
215 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
216 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
217 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
218 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
219 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
220 </param>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
221 </when>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
222 </conditional>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
223 </when>
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
224 </conditional>
0
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
225 <section name="annotation_options" expanded="false" title="Annotation Options">
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
226 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
227 <option value="NOG">All organisms (NOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
228 <option value="aciNOG">Acidobacteria (aciNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
229 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
230 <option value="acoNOG">Aconoidasida (acoNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
231 <option value="actNOG">Actinobacteria (actNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
232 <option value="agaNOG">Agaricales (agaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
233 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
234 <option value="apiNOG">Apicomplexa (apiNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
235 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
236 <option value="aquNOG">Aquificae (aquNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
237 <option value="arNOG">Archaea (arNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
238 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
239 <option value="artNOG">Arthropoda (artNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
240 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
241 <option value="ascNOG">Ascomycota (ascNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
242 <option value="aveNOG">Aves (aveNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
243 <option value="bacNOG">Bacilli (bacNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
244 <option value="bactNOG">Bacteria (bactNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
245 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
246 <option value="basNOG">Basidiomycota (basNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
247 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
248 <option value="biNOG">Bilateria (biNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
249 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
250 <option value="braNOG">Brassicales (braNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
251 <option value="carNOG">Carnivora (carNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
252 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
253 <option value="chlNOG">Chlorobi (chlNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
254 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
255 <option value="chloNOG">Chloroflexi (chloNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
256 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
257 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
258 <option value="chorNOG">Chordata (chorNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
259 <option value="chrNOG">Chromadorea (chrNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
260 <option value="cloNOG">Clostridia (cloNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
261 <option value="cocNOG">Coccidia (cocNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
262 <option value="creNOG">Crenarchaeota (creNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
263 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
264 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
265 <option value="cytNOG">Cytophagia (cytNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
266 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
267 <option value="defNOG">Deferribacteres (defNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
268 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
269 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
270 <option value="delNOG">delta/epsilon (delNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
271 <option value="dipNOG">Diptera (dipNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
272 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
273 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
274 <option value="droNOG">Drosophilidae (droNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
275 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
276 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
277 <option value="euNOG">Eukaryotes (euNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
278 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
279 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
280 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
281 <option value="fiNOG">Fishes (fiNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
282 <option value="firmNOG">Firmicutes (firmNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
283 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
284 <option value="fuNOG">Fungi (fuNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
285 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
286 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
287 <option value="haeNOG">Haemosporida (haeNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
288 <option value="halNOG">Halobacteria (halNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
289 <option value="homNOG">Hominidae (homNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
290 <option value="hymNOG">Hymenoptera (hymNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
291 <option value="hypNOG">Hypocreales (hypNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
292 <option value="inNOG">Insects (inNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
293 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
294 <option value="lepNOG">Lepidoptera (lepNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
295 <option value="lilNOG">Liliopsida (lilNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
296 <option value="maNOG">Mammals (maNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
297 <option value="magNOG">Magnaporthales (magNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
298 <option value="meNOG">Animals (meNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
299 <option value="metNOG">Methanobacteria (metNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
300 <option value="methNOG">Methanococci (methNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
301 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
302 <option value="necNOG">Nectriaceae (necNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
303 <option value="negNOG">Negativicutes (negNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
304 <option value="nemNOG">Nematodes (nemNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
305 <option value="onyNOG">Onygenales (onyNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
306 <option value="opiNOG">Opisthokonts (opiNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
307 <option value="perNOG">Peronosporales (perNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
308 <option value="plaNOG">Planctomycetes (plaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
309 <option value="pleNOG">Pleosporales (pleNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
310 <option value="poaNOG">Poales (poaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
311 <option value="prNOG">Primates (prNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
312 <option value="proNOG">Proteobacteria (proNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
313 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
314 <option value="roNOG">Rodents (roNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
315 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
316 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
317 <option value="sorNOG">Sordariales (sorNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
318 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
319 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
320 <option value="spiNOG">Spirochaetes (spiNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
321 <option value="spriNOG">Supraprimates (spriNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
322 <option value="strNOG">Streptophyta (strNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
323 <option value="synNOG">Synergistetes (synNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
324 <option value="tenNOG">Tenericutes (tenNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
325 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
326 <option value="theNOG">Thermoplasmata (theNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
327 <option value="therNOG">Thermotogae (therNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
328 <option value="thermNOG">Thermococci (thermNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
329 <option value="treNOG">Tremellales (treNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
330 <option value="veNOG">Vertebrates (veNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
331 <option value="verNOG">Verrucomicrobia (verNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
332 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
333 <option value="virNOG">Viridiplantae (virNOG)</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
334 </param>
2
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
335 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
0
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
336 <option value="one2one">one2one</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
337 <option value="many2one">many2one</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
338 <option value="one2many">one2many</option>
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
339 <option value="many2many">many2many</option>
2
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
340 <option value="all" selected="true">all</option>
0
b3ae16ffb54e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper
jjohnson
parents:
diff changeset
341 </param>
2
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
342 <param name="go_evidence" type="select"
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
parents: 1
diff changeset
343 label="Select the set of GO terms that should be used for annotation">
0
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344 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
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345 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
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346 </param>
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347 </section>
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348 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
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349 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
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350 <help>
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351 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
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352 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
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353 </help>
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354 </param>
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355 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
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356 <help>
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357 Min bit score expected when searching for seed eggNOG ortholog.
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358 Queries not having a significant seed orthologs will not be annotated.
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359 </help>
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360 </param>
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361 </section>
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362 <section name="output_options" expanded="false" title="Output Options">
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363 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
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364 label="Exclude header lines and stats from output files"/>
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365 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
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366 label="Skip functional annotation, reporting only hits"/>
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367 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
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368 label="Output a file with the list of orthologs for each hits"/>
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369 </section>
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370 </inputs>
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371 <outputs>
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372 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
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373 <actions>
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374 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
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375 </actions>
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376 </data>
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377 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
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378 <filter>not output_options['no_annot']</filter>
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379 <actions>
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380 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_KO,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_HMM_model_annotation"/>
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381 </actions>
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382 </data>
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383 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits">
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384 <filter>db['mode'] == 'hmmer'</filter>
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385 <actions>
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386 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
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387 </actions>
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388 </data>
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389 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
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390 <filter>output_options['report_orthologs']</filter>
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391 <actions>
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392 <action name="column_names" type="metadata" default="query_name,orthologs"/>
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393 </actions>
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394 </data>
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395 </outputs>
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396 <tests>
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397 <test>
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398 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
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399 <param name="database" value="ENOG411CB2I"/>
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400 <param name="mode" value="hmmer"/>
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401 <!--
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402 <param name="test" value="true"/>
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403 -->
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404 <param name="eggnog_data" value="4.5"/>
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405 <param name="no_annot" value="true"/>
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406 <param name="no_file_comments" value="true"/>
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407 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
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408 </test>
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409 <test>
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410 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
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411 <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work -->
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412 <param name="no_annot" value="true"/>
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413 <param name="mode" value="diamond"/>
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414 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
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415 </test>
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416 </tests>
0
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417 <help><![CDATA[
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418
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419 eggnog-mapper
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420 =============
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421 Overview
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422 --------
0
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423
2
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424 ``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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425 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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426 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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427 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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428
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429 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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430
2
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431 Options
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432 -------
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433
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434 ``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_.
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435 HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences.
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436
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437
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438 Outputs
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439 -------
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440
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441 **hmm_hits**
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442
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443 For each query sequence, a list of significant
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444 hits to eggNOG Orthologous Groups (OGs) is reported.
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445 Each line in the file represents a hit, where evalue, bit-score,
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446 query-coverage and the sequence coordinates of the match are reported.
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447 If multiple hits exist for a given query, results are sorted by e-value.
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448 Only returned when using HMMER mode.
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449
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450 **seed_orthologs**
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451
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452 each line in the file provides the best match of each query within the best Orthologous Group (OG)
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453 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
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454 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
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455 If using the diamond search mode, seed orthologs are directly
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456 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
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457
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458 **annotations**
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459
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460 This file provides final annotations of each query. Tab-delimited columns in the file are:
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461
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462 - ``query_name``: query sequence name
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463 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
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464 - ``seed_ortholog_evalue``: best protein match (e-value)
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465 - ``seed_ortholog_score``: best protein match (bit-score)
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466 - ``predicted_gene_name``: Predicted gene name for query sequences
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467 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
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468 - ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
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469 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
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470 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
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471 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
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472 - ``COG functional categories``: COG functional category inferred from best matching OG
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473 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
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474
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475 ]]></help>
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476 <expand macro="citations"/>
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477 </tool>