eggnog_mapper: eggnog_mapper.xml annotate

annotate eggnog_mapper.xml @ 6:3cb37af59360 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"

author	galaxyp
date	Sat, 05 Sep 2020 07:21:28 +0000
parents	a5a3bdd0954b
children	4e4c6329f6cd

rev	line source
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	1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	2 <description>functional sequence annotation by orthology</description>
4 2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99 galaxyp parents: 3 diff changeset	3 <macros>
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	4 <import>eggnog_macros.xml</import>
4 2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99 galaxyp parents: 3 diff changeset	5 </macros>
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	6 <expand macro="requirements"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	7 <expand macro="version_command"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	8 <command detect_errors="aggressive"><![CDATA[
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	9 emapper.py
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	10 --data_dir '$eggnog_data.fields.path'
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	11 -m diamond
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	12 $translate
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	13
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	14 ## Diamond option
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	15 --matrix '$diamond.matrix_gapcosts.matrix'
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	16 $diamond.matrix_gapcosts.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	17 --query-cover $diamond.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	18 --subject-cover $diamond.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	19
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	20 #if $annotation_options.tax_scope:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	21 --tax_scope=$annotation_options.tax_scope
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	22 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	23 #if $annotation_options.target_orthologs:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	24 --target_orthologs=$annotation_options.target_orthologs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	25 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	26 #if $annotation_options.go_evidence:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	27 --go_evidence=$annotation_options.go_evidence
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	28 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	29 #if $seed_ortholog_options.seed_ortholog_evalue:
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	30 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	31 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	32 #if str($seed_ortholog_options.seed_ortholog_score):
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	33 --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	34 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	35 $output_options.no_file_comments
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	36 $output_options.no_annot
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	37 $output_options.report_orthologs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	38 --output='results'
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	39 -i '${input}'
1 3c7c9396daaa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9505f2a447df1bcd46ceca7b5ddb532a2f8a1cd1 galaxyp parents: 0 diff changeset	40 --cpu "\${GALAXY_SLOTS:-4}"
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	41 ]]></command>
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	42 <inputs>
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	43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
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	44 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
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	45 <options from_data_table="eggnog_mapper_db"/>
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	46 </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	47 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
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	48 label="Are these coding DNA sequences that need to be translated?"/>
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	49
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	50 <section name="diamond" expanded="true" title="Diamond Options">
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	51 <conditional name="matrix_gapcosts">
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	52 <param argument="--matrix" type="select" label="Scoring matrix and 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	53 <option value="BLOSUM90">BLOSUM90</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	54 <option value="BLOSUM80">BLOSUM80</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	55 <option value="BLOSUM62" selected="true">BLOSUM62</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	56 <option value="BLOSUM50">BLOSUM50</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	57 <option value="BLOSUM45">BLOSUM45</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	58 <option value="PAM250">PAM250</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	59 <option value="PAM70">PAM70</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	60 <option value="PAM30">PAM30</option>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	61 </param>
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	62 <when value="BLOSUM90">
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	63 <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	64 <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	65 <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	66 <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	67 <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	68 <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	69 <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	70 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	71 </param>
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	72 </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	73 <when value="BLOSUM80">
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	74 <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	75 <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	76 <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	77 <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	78 <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	79 <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	80 <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	81 </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	82 </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	83 <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	84 <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	85 <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	86 <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	87 <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	88 <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	89 <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	90 <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	91 <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	92 <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	93 <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	94 <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	95 <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	96 </param>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	97 </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	98 <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	99 <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	100 <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	101 <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	102 <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	103 <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	104 <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	105 <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	106 <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	107 <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	108 <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	109 <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	110 <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	111 <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	112 <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	113 <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	114 <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	115 </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	116 </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	117 <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	118 <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	119 <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	120 <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	121 <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	122 <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	123 <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	124 <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	125 <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	126 <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	127 <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	128 <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	129 <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	130 <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	131 </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	132 </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	133 <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	134 <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	135 <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	136 <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	137 <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	138 <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	139 <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	140 <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	141 <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	142 <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	143 <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	144 <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	145 <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	146 <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	147 <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	148 <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	149 </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	150 </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	151 <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	152 <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	153 <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	154 <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	155 <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	156 <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	157 <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	158 <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	159 <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	160 <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	161 </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	162 </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	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 <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	171 <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	172 <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	173 <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	174 <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	175 </param>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	176 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	177 </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 diff changeset	178
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	179 <param name="query_cover" type="integer" value="0" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
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	180 <param name="subject_cover" type="integer" value="0" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
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 </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	182
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	183 <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	184 <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 parents: diff changeset	185 <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	186 <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	187 <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	188 <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	189 <option value="many2many">many2many</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="all" selected="true">all</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	191 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	192 <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 parents: diff changeset	193 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 parents: diff changeset	194 <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 parents: diff changeset	195 <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 parents: diff changeset	196 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	197 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	198 <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 parents: diff changeset	199 <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 galaxyp parents: diff changeset	200 <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	201 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 galaxyp parents: diff changeset	202 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 parents: diff changeset	203 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	204 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	205 <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 parents: diff changeset	206 <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	207 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 galaxyp parents: diff changeset	208 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 parents: diff changeset	209 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	210 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	211 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	212 <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 parents: diff changeset	213 <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 parents: diff changeset	214 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 parents: diff changeset	215 <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 parents: diff changeset	216 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 parents: diff changeset	217 <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 galaxyp parents: diff changeset	218 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 galaxyp parents: diff changeset	219 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	220 </inputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	221 <outputs>
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	222 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	223 <actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	224 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	225 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	226 </data>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	227 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	228 <filter>not output_options['no_annot']</filter>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	229 <actions>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	230 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_taxonomic_group,predicted_protein_name,GO_terms,EC_number,KEGG_KO,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG\|evalue\|score,COG_functional_categories,eggNOG_free_text_description"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	231 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	232 </data>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	233 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	234 <filter>output_options['report_orthologs']</filter>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	235 <actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	236 <action name="column_names" type="metadata" default="query_name,orthologs"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	237 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	238 </data>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	239 </outputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	240 <tests>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	241 <test>
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	242 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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	243 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	244 <param name="no_annot" value="true"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	245 <param name="no_file_comments" value="true"/>
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	246 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	247 </test>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	248 <test>
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	249 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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	250 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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	251 <param name="report_orthologs" value="true"/>
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	252 <param name="no_file_comments" value="true"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	253 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
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	254 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular"/>
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	255 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
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	256 </test>
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	257 <test>
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	258 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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	259 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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	260 <param name="report_orthologs" value="true"/>
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	261 <param name="no_file_comments" value="true"/>
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	262 <section name="annotation_options">
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	263 <param name="tax_scope" value="651137" />
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	264 </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	265 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular"/>
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	266 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular"/>
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	267 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	268 </test>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	269 </tests>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	270 <help><![CDATA[
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	271
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	272 eggnog-mapper
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	273 =============
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	274 Overview
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	275 --------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	276
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	277 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
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	278 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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	279 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	280 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	281
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	282 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	283
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	284 Outputs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	285 -------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	286
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	287 seed_orthologs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	288
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	289 each line in the file provides the best match of each query within the best Orthologous Group (OG)
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	290 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
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	291 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
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	292 If using the diamond search mode, seed orthologs are directly
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	293 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	294
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	295 annotations
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	296
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	297 This file provides final annotations of each query. Tab-delimited columns in the file are:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	298
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	299 - ``query_name``: query sequence name
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	300 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	301 - ``seed_ortholog_evalue``: best protein match (e-value)
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	302 - ``seed_ortholog_score``: best protein match (bit-score)
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	303 - ``predicted_taxonomic_group``
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	304 - ``predicted_protein_name``: Predicted protein name for query sequences
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	305 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
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	306 - ``EC_number``
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	307 - ``KEGG_KO``
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	308 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
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	309 - ``KEGG_Module``
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	310 - ``KEGG_Reaction``
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	311 - ``KEGG_rclass``
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	312 - ``BRITE``
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	313 - ``KEGG_TC``
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	314 - ``CAZy``
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	315 - ``BiGG_Reactions``
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	316 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	317 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
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	318 - ``best_OG\|evalue\|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
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	319 - ``COG_functional_categories``: COG functional category inferred from best matching OG
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	320 - ``eggNOG_free_text_description``
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	321
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	322 ]]></help>
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	323 <expand macro="citations"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	324 </tool>

Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 6:3cb37af59360 draft