Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 7:4e4c6329f6cd draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author galaxyp
date Fri, 19 Feb 2021 18:54:25 +0000
parents 3cb37af59360
children 96cac424c870
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rev   line source
7
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy1">
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2 <description>functional sequence annotation by orthology</description>
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3 <macros>
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a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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4 <import>eggnog_macros.xml</import>
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5 </macros>
5
a5a3bdd0954b "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 diamond
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12 $translate
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3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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14 ## Diamond option
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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15 --matrix '$diamond.matrix_gapcosts.matrix'
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16 $diamond.matrix_gapcosts.gap_costs
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17 --query-cover $diamond.query_cover
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18 --subject-cover $diamond.subject_cover
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19
0
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20 #if $annotation_options.tax_scope:
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21 --tax_scope=$annotation_options.tax_scope
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22 #end if
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23 #if $annotation_options.target_orthologs:
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24 --target_orthologs=$annotation_options.target_orthologs
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25 #end if
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26 #if $annotation_options.go_evidence:
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27 --go_evidence=$annotation_options.go_evidence
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28 #end if
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29 #if $seed_ortholog_options.seed_ortholog_evalue:
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30 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
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31 #end if
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32 #if str($seed_ortholog_options.seed_ortholog_score):
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33 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
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34 #end if
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35 $output_options.no_file_comments
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36 $output_options.no_annot
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37 $output_options.report_orthologs
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38 --output='results'
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39 -i '${input}'
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40 --cpu "\${GALAXY_SLOTS:-4}"
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41 ]]></command>
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42 <inputs>
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43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
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44 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
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4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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45 <options from_data_table="eggnog_mapper_db_versioned">
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46 <filter type="static_value" column="3" value="@IDX_VERSION@" />
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47 </options>
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48 </param>
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49 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
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50 label="Are these coding DNA sequences that need to be translated?"/>
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51
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52 <section name="diamond" expanded="true" title="Diamond Options">
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53 <conditional name="matrix_gapcosts">
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54 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
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55 <option value="BLOSUM90">BLOSUM90</option>
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56 <option value="BLOSUM80">BLOSUM80</option>
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57 <option value="BLOSUM62" selected="true">BLOSUM62</option>
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58 <option value="BLOSUM50">BLOSUM50</option>
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59 <option value="BLOSUM45">BLOSUM45</option>
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60 <option value="PAM250">PAM250</option>
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61 <option value="PAM70">PAM70</option>
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62 <option value="PAM30">PAM30</option>
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63 </param>
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64 <when value="BLOSUM90">
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65 <param name="gap_costs" type="select" label="Gap Costs">
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66 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
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67 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
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68 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
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69 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
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70 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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71 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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72 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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73 </param>
6
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74 </when>
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75 <when value="BLOSUM80">
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diff changeset
76 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
77 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
78 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
79 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
80 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
81 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
82 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
83 </param>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
84 </when>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
85 <when value="BLOSUM62">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
86 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
87 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
88 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
89 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
90 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
91 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
92 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
93 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
94 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
95 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
96 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
97 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
98 </param>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
99 </when>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
100 <when value="BLOSUM50">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
101 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
102 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
103 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
104 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
105 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
106 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
107 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
108 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
109 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
110 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
111 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
112 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
113 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
114 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
115 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
116 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
117 </param>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
118 </when>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
119 <when value="BLOSUM45">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
120 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
121 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
122 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
123 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
124 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
125 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
126 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
127 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
128 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
129 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
130 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
131 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
132 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
133 </param>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
134 </when>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
135 <when value="PAM250">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
136 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
137 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
138 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
139 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
140 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
141 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
142 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
143 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
144 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
145 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
146 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
147 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
148 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
149 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
150 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
151 </param>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
152 </when>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
153 <when value="PAM70">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
154 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
155 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
156 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
157 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
158 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
159 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
160 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
161 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
162 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
163 </param>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
164 </when>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
165 <when value="PAM30">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
166 <param name="gap_costs" type="select" label="Gap Costs">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
167 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
168 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
169 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
170 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
171 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
172 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
173 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
174 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
175 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
176 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
177 </param>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
178 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
179 </conditional>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
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180
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
181 <param name="query_cover" type="integer" value="0" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
182 <param name="subject_cover" type="integer" value="0" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
183 </section>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
184
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
185 <section name="annotation_options" expanded="false" title="Annotation Options">
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
186 <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
187 <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
188 <option value="one2one">one2one</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
189 <option value="many2one">many2one</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
190 <option value="one2many">one2many</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
191 <option value="many2many">many2many</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
192 <option value="all" selected="true">all</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
193 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
194 <param name="go_evidence" type="select"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
195 label="Select the set of GO terms that should be used for annotation">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
196 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
197 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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198 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
199 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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200 <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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201 <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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202 <help>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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diff changeset
203 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
204 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
205 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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206 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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207 <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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208 <help>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
209 Min bit score expected when searching for seed eggNOG ortholog.
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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210 Queries not having a significant seed orthologs will not be annotated.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
211 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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212 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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213 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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214 <section name="output_options" expanded="false" title="Output Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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215 <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
216 label="Exclude header lines and stats from output files"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
217 <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
218 label="Skip functional annotation, reporting only hits"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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219 <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
220 label="Output a file with the list of orthologs for each hits"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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221 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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222 </inputs>
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223 <outputs>
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224 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
0
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225 <actions>
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226 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
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227 </actions>
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228 </data>
6
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229 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
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230 <filter>not output_options['no_annot']</filter>
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231 <actions>
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232 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_taxonomic_group,predicted_protein_name,GO_terms,EC_number,KEGG_KO,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_free_text_description"/>
0
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233 </actions>
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234 </data>
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235 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
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236 <filter>output_options['report_orthologs']</filter>
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237 <actions>
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238 <action name="column_names" type="metadata" default="query_name,orthologs"/>
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239 </actions>
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240 </data>
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241 </outputs>
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242 <tests>
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243 <test>
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244 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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245 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
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246 <param name="no_annot" value="true"/>
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247 <param name="no_file_comments" value="true"/>
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248 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
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249 </test>
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250 <test>
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251 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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252 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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253 <param name="report_orthologs" value="true"/>
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254 <param name="no_file_comments" value="true"/>
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255 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
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256 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
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257 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
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258 </test>
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259 <test>
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260 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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261 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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262 <param name="report_orthologs" value="true"/>
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263 <param name="no_file_comments" value="true"/>
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264 <section name="annotation_options">
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265 <param name="tax_scope" value="651137" />
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266 </section>
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267 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
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268 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/>
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269 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
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270 </test>
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271 </tests>
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272 <help><![CDATA[
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273
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274 eggnog-mapper
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275 =============
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276 Overview
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277 --------
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278
6
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279 ``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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280 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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281 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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282 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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283
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284 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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285
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286 Outputs
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287 -------
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288
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289 **seed_orthologs**
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290
6
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291 each line in the file provides the best match of each query within the best Orthologous Group (OG)
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292 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
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293 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
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294 If using the diamond search mode, seed orthologs are directly
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295 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
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296
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297 **annotations**
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298
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299 This file provides final annotations of each query. Tab-delimited columns in the file are:
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300
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301 - ``query_name``: query sequence name
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302 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
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303 - ``seed_ortholog_evalue``: best protein match (e-value)
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304 - ``seed_ortholog_score``: best protein match (bit-score)
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305 - ``predicted_taxonomic_group``
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306 - ``predicted_protein_name``: Predicted protein name for query sequences
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307 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
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308 - ``EC_number``
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309 - ``KEGG_KO``
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310 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
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311 - ``KEGG_Module``
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312 - ``KEGG_Reaction``
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313 - ``KEGG_rclass``
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314 - ``BRITE``
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315 - ``KEGG_TC``
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316 - ``CAZy``
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317 - ``BiGG_Reactions``
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318 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
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319 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
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320 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
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321 - ``COG_functional_categories``: COG functional category inferred from best matching OG
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322 - ``eggNOG_free_text_description``
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323
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324 ]]></help>
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325 <expand macro="citations"/>
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326 </tool>