Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 9:bb2fd26a081d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 622d8d475193f3717d26f45fd7c8f5868e9a2d0d
author galaxyp
date Tue, 07 Jun 2022 14:56:07 +0000
parents cc203b7580e7
children 3d30526975d7
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9
bb2fd26a081d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 622d8d475193f3717d26f45fd7c8f5868e9a2d0d
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy2">
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2 <description>functional sequence annotation by orthology</description>
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3 <macros>
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4 <import>eggnog_macros.xml</import>
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5 </macros>
5
59501122d153 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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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 '$eggnog_data.fields.path'
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11 -m '$seed_ortho_options.ortho_method.m'
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12 --itype '${input_trans.itype}'
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13 #if $input_trans.itype in ['CDS', 'genome', 'metagenome']:
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14 $input_trans.translate
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15 #end if
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16 #if $input_trans.itype in ['genome', 'metagenome']:
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17 --genepred $input_trans.genepred
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18 #end if
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20 ## Diamond option
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21 #if $seed_ortho_options.ortho_method.m == "diamond":
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22 --matrix '$seed_ortho_options.ortho_method.matrix_gapcosts.matrix'
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23 $seed_ortho_options.ortho_method.matrix_gapcosts.gap_costs
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24 --sensmode $seed_ortho_options.ortho_method.sensmode
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25 $seed_ortho_options.ortho_method.dmnd_iterate
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26 $seed_ortho_options.ortho_method.dmnd_ignore_warnings
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27 #elif $seed_ortho_options.ortho_method.m == "mmseqs":
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28 --start_sens $seed_ortho_options.ortho_method.start_sens
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29 --sens_steps $seed_ortho_options.ortho_method.sens_steps
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30 --final_sens $seed_ortho_options.ortho_method.final_sens
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31 #end if
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32
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33 ## Common options for search filtering
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34 #if $seed_ortho_options.query_cover:
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35 --query_cover $seed_ortho_options.query_cover
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36 #end if
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37 #if $seed_ortho_options.subject_cover:
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38 --subject_cover $seed_ortho_options.subject_cover
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39 #end if
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40 #if $seed_ortho_options.pident:
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41 --pident $seed_ortho_options.pident
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42 #end if
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43
0
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44 #if $annotation_options.tax_scope:
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45 --tax_scope=$annotation_options.tax_scope
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46 #end if
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47 #if $annotation_options.target_orthologs:
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48 --target_orthologs=$annotation_options.target_orthologs
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49 #end if
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50 #if $annotation_options.go_evidence:
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51 --go_evidence=$annotation_options.go_evidence
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52 #end if
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53 #if $seed_ortholog_options.seed_ortholog_evalue:
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54 --evalue=$seed_ortholog_options.seed_ortholog_evalue
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55 #end if
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56 #if str($seed_ortholog_options.seed_ortholog_score):
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57 --score=$seed_ortholog_options.seed_ortholog_score
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58 #end if
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59 $output_options.no_file_comments
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60 $output_options.no_annot
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61 $output_options.report_orthologs
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62 --output='results'
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63 -i '${input}'
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64 --cpu "\${GALAXY_SLOTS:-4}"
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65 ]]></command>
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66 <inputs>
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67 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
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68 <conditional name="input_trans">
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69 <param argument="--itype" type="select" label="Type of sequences">
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70 <option value="proteins" selected="true">proteins</option>
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71 <option value="CDS">CDS</option>
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72 <option value="genome">genome</option>
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73 <option value="metagenome">metagenome</option>
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74 </param>
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75 <when value="proteins"/>
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76 <when value="CDS">
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77 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
78 label="Translate CDS to proteins before search"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
79 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
80 <when value="genome">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
81 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
82 label="Translate predicted CDS from blastx hits to proteins"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
83 <param argument="--genepred" type="select" label="Type of sequences">
9
bb2fd26a081d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 622d8d475193f3717d26f45fd7c8f5868e9a2d0d
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diff changeset
84 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
bb2fd26a081d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 622d8d475193f3717d26f45fd7c8f5868e9a2d0d
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parents: 8
diff changeset
85 <option value="prodigal" selected="true">Performed using Prodigal</option>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
86 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
87 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
88 <when value="metagenome">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
89 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
90 label="Translate predicted CDS from blastx hits to proteins"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
91 <param argument="--genepred" type="select" label="Type of sequences">
9
bb2fd26a081d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 622d8d475193f3717d26f45fd7c8f5868e9a2d0d
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parents: 8
diff changeset
92 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
bb2fd26a081d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 622d8d475193f3717d26f45fd7c8f5868e9a2d0d
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parents: 8
diff changeset
93 <option value="prodigal" selected="true">Performed using Prodigal</option>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
94 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
95 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
96 </conditional>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
97 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
98 <options from_data_table="eggnog_mapper_db_versioned">
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
99 <filter type="static_value" column="3" value="@IDX_VERSION@" />
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
100 </options>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
101 </param>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
102
7
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diff changeset
103 <section name="seed_ortho_options" expanded="true" title="Seed orthologs search options">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
104 <conditional name="ortho_method">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
105 <param argument="-m" type="select" label="Method to search seed orthologs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
106 <option value="diamond" selected="true">Diamond</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
107 <option value="mmseqs">MMseqs2</option>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
108 </param>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
109 <when value="diamond">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
110 <conditional name="matrix_gapcosts">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
111 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
112 <option value="BLOSUM90">BLOSUM90</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
113 <option value="BLOSUM80">BLOSUM80</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
114 <option value="BLOSUM62" selected="true">BLOSUM62</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
115 <option value="BLOSUM50">BLOSUM50</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
116 <option value="BLOSUM45">BLOSUM45</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
117 <option value="PAM250">PAM250</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
118 <option value="PAM70">PAM70</option>
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diff changeset
119 <option value="PAM30">PAM30</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
120 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
121 <when value="BLOSUM90">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
122 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
123 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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124 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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125 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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126 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
127 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
128 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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129 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
130 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
131 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
132 <when value="BLOSUM80">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
133 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
134 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
135 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
136 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
137 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
138 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
139 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
140 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
141 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
142 <when value="BLOSUM62">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
143 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
144 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
145 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
146 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
147 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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parents: 6
diff changeset
148 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
149 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
150 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
151 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
152 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
153 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
154 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
155 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
156 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
157 <when value="BLOSUM50">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
158 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
159 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
160 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
161 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
162 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
163 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
164 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
165 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
166 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
167 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
168 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
169 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
170 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
171 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
172 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
173 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
174 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
175 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
176 <when value="BLOSUM45">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
177 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
178 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
179 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
180 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
181 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
182 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
183 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
184 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
185 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
186 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
187 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
188 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
189 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
190 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
191 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
192 <when value="PAM250">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
193 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
194 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
195 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
196 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
197 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
198 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
199 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
200 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
201 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
202 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
203 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
204 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
205 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
206 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
207 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
208 </param>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
209 </when>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
210 <when value="PAM70">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
211 <param name="gap_costs" type="select" label="Gap Costs">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
212 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
213 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
214 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
215 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
216 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
217 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
218 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
219 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
220 </param>
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galaxyp
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221 </when>
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diff changeset
222 <when value="PAM30">
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diff changeset
223 <param name="gap_costs" type="select" label="Gap Costs">
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galaxyp
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224 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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225 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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226 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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227 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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228 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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229 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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230 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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231 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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232 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
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galaxyp
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233 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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234 </param>
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235 </when>
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236 </conditional>
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237 <param name="sensmode" type="select" label="Gap Costs">
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238 <option value="default">default</option>
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239 <option value="fast">fast</option>
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240 <option value="mid-sensitive">mid-sensitive</option>
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241 <option value="sensitive" selected="true">sensitive</option>
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242 <option value="more-sensitive">more-sensitive</option>
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243 <option value="very-sensitive">very-sensitive</option>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
244 <option value="ultra-sensitive">ultra-sensitive</option>
0
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245 </param>
7
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diff changeset
246 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false"
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
247 label="Run diamond in iterative mode, up to the sensitivity level"/>
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248 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false"
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
249 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/>
0
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250 </when>
7
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diff changeset
251 <when value="mmseqs">
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252 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" />
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diff changeset
253 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" />
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
254 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" />
0
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255 </when>
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256 </conditional>
6
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257
7
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diff changeset
258 <param argument="--query_cover" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
259 <param argument="--subject_cover" type="integer" optional="true" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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260 <param argument="--pident" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of identity" />
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
261 </section>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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262
0
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263 <section name="annotation_options" expanded="false" title="Annotation Options">
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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264 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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265 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
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266 <option value="one2one">one2one</option>
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267 <option value="many2one">many2one</option>
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268 <option value="one2many">one2many</option>
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269 <option value="many2many">many2many</option>
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270 <option value="all" selected="true">all</option>
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271 </param>
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272 <param name="go_evidence" type="select"
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273 label="Select the set of GO terms that should be used for annotation">
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274 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
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275 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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276 <option value="all" selected="true">All (experimental + non-electronic)</option>
0
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277 </param>
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278 </section>
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279 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
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280 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
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281 <help>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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282 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
0
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283 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
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284 </help>
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285 </param>
7
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286 <param name="seed_ortholog_score" type="integer" optional="true" min="0" label="Minimum bit score threshold">
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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287 <help>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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288 Min bit score expected when searching for seed eggNOG ortholog.
0
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289 Queries not having a significant seed orthologs will not be annotated.
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290 </help>
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291 </param>
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292 </section>
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293 <section name="output_options" expanded="false" title="Output Options">
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294 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
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295 label="Exclude header lines and stats from output files"/>
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galaxyp
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296 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
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297 label="Skip functional annotation, reporting only hits"/>
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298 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
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299 label="Output a file with the list of orthologs for each hits"/>
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300 </section>
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301 </inputs>
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302 <outputs>
6
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303 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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304 <actions>
7
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305 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov"/>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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306 </actions>
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307 </data>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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308 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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309 <filter>not output_options['no_annot']</filter>
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310 <actions>
7
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311 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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312 </actions>
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313 </data>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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314 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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315 <filter>output_options['report_orthologs']</filter>
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316 <actions>
7
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317 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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318 </actions>
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319 </data>
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320 </outputs>
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321 <tests>
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322 <test>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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323 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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324 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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325 <param name="no_annot" value="true"/>
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326 <param name="no_file_comments" value="true"/>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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327 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
0
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328 </test>
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329 <test>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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330 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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331 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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332 <param name="report_orthologs" value="true"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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333 <param name="no_file_comments" value="true"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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334 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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335 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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336 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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337 </test>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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338 <test>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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339 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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340 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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341 <param name="report_orthologs" value="true"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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342 <param name="no_file_comments" value="true"/>
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343 <section name="annotation_options">
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344 <param name="tax_scope" value="651137" />
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345 </section>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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346 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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347 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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348 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
0
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349 </test>
7
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350 <test>
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351 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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352 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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353 <section name="seed_ortho_options">
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354 <conditional name="ortho_method">
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355 <param name="m" value="diamond" />
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356 <param name="sensmode" value="fast" />
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357 </conditional>
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358 </section>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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359 <param name="report_orthologs" value="true"/>
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360 <param name="no_file_comments" value="true"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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361 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
362 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
363 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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364 </test>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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365 <!-- not enabled as it requires a specific .db file, hard to minimize -->
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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366 <!--test>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
367 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
368 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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369 <section name="seed_ortho_options">
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370 <conditional name="ortho_method">
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371 <param name="m" value="mmseqs" />
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372 <param name="start_sens" value="4" />
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373 </conditional>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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374 </section>
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375 <param name="report_orthologs" value="true"/>
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376 <param name="no_file_comments" value="true"/>
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377 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
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378 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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379 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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380 </test-->
0
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381 </tests>
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382 <help><![CDATA[
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383
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384 eggnog-mapper
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385 =============
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386 Overview
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387 --------
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388
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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389 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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390 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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391 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
0
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392 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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393
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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394 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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395
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396 Outputs
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397 -------
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398
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399 **seed_orthologs**
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400
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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401 each line in the file provides the best match of each query within the best Orthologous Group (OG)
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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402 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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403 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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404 If using the diamond search mode, seed orthologs are directly
0
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405 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
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406
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407 **annotations**
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408
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409 This file provides final annotations of each query. Tab-delimited columns in the file are:
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410
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411 - ``query_name``: query sequence name
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412 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
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413 - ``seed_ortholog_evalue``: best protein match (e-value)
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414 - ``seed_ortholog_score``: best protein match (bit-score)
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415 - ``predicted_taxonomic_group``
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416 - ``predicted_protein_name``: Predicted protein name for query sequences
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417 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
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1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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418 - ``EC_number``
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419 - ``KEGG_KO``
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420 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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421 - ``KEGG_Module``
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422 - ``KEGG_Reaction``
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423 - ``KEGG_rclass``
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424 - ``BRITE``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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425 - ``KEGG_TC``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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426 - ``CAZy``
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427 - ``BiGG_Reactions``
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428 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
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429 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
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1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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430 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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431 - ``COG_functional_categories``: COG functional category inferred from best matching OG
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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432 - ``eggNOG_free_text_description``
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433
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434 ]]></help>
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59501122d153 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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435 <expand macro="citations"/>
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436 </tool>