eggnog_mapper: eggnog_mapper.xml annotate

author	galaxyp
date	Tue, 31 Oct 2017 14:17:50 -0400
parents
children	3c7c9396daaa

rev	line source
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="1.0.1">
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>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	3 <requirements>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	4 <requirement type="package" version="1.0.1">eggnog-mapper</requirement>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	5 </requirements>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	6 <version_command>emapper.py --version</version_command>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	7 <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	8 emapper.py
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	9 --data_dir '$eggnog_data.fields.db'
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	10 -m $db.mode
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	11 $translate
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	12 #if ($db.mode == 'hmmer'):
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	13 --database=$db.database.fields.db
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	14 #if $db.hmm_options.hmm_settings == 'specified':
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	15 --hmm_maxhits=$db.hmm_options.hmm_maxhits
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	16 --hmm_evalue=$db.hmm_options.hmm_evalue
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	17 --hmm_score=$db.hmm_options.hmm_score
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	18 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	19 #if str($db.hmm_options.hmm_qcov):
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	20 --hmm_qcov=$db.hmm_options.hmm_qcov
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	21 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	22 --Z=$db.hmm_options.Z
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	23 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	24 #elif ($db.mode == 'diamond'):
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	25 --matrix '$db.matrix_gapcosts.matrix'
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	26 $db.matrix_gapcosts.gap_costs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	27 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	28 #if $annotation_options.tax_scope:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	29 --tax_scope=$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	30 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	31 #if $annotation_options.target_orthologs:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	32 --target_orthologs=$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	33 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	34 #if $annotation_options.go_evidence:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	35 --go_evidence=$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	36 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	37 #if $seed_ortholog_options.seed_ortholog_evalue:
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	38 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	39 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	40 #if str($seed_ortholog_options.seed_ortholog_score):
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	41 --seed_ortholog_score=$seed_ortholog_options.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	42 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	43 $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	44 $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	45 $output_options.report_orthologs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	46 --output='results'
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	47 -i '${input}'
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	48 ]]></command>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	49 <inputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	50 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	51 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	52 <options from_data_table="eggnog_mapper">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	53 <filter type="static_value" name="type" value="data" column="2"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	54 </options>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	55 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	56 <param name="translate" type="boolean" truevalue="--translate" 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	57 label="Are these coding DNA sequences that need to be translated?"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	58 <conditional name="db">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	59 <param name="mode" type="select" label="Annotation Type">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	60 <option value="hmmer">HMM</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	61 <option value="diamond">DIAMOND</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	62 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	63 <when value="hmmer">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	64 <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed.">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	65 <options from_data_table="eggnog_mapper">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	66 <filter type="static_value" value="hmmer" column="2"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	67 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	68 </options>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	69 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	70 <conditional name="hmm_options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	71 <param name="hmm_settings" type="select" label="HMM Search Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	72 <option value="default">Use defaults</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	73 <option value="specified">Set HMM Search Options</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	74 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	75 <when value="default"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	76 <when value="specified">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	77 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	78 <param name="hmm_evalue" type="float" min="0" value="0.001" label="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	79 <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	80 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	81 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	82 <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" />
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	83 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	84 </conditional>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	85 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	86 <when value="diamond">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	87 <!-- db.database is used in diamond mode only to name outputs -->
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	88 <param name="database" type="hidden" value="diamond"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	89 <conditional name="matrix_gapcosts">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	90 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	91 <option value="BLOSUM90">BLOSUM90</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	92 <option value="BLOSUM80">BLOSUM80</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	93 <option value="BLOSUM62" selected="true">BLOSUM62</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	94 <option value="BLOSUM50">BLOSUM50</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	95 <option value="BLOSUM45">BLOSUM45</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	96 <option value="PAM250">PAM250</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	97 <option value="PAM70">PAM70</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	98 <option value="PAM30">PAM30</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	99 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	100 <when value="BLOSUM90">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	101 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	102 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	103 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	104 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	105 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	106 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	107 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	108 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	109 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	110 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	111 <when value="BLOSUM80">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	112 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	113 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	114 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	115 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	116 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	117 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	118 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	119 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	120 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	121 <when value="BLOSUM62">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	122 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	123 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	124 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	125 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	126 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	127 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	128 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	129 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	130 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	131 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	132 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	134 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	135 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	136 <when value="BLOSUM50">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	137 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	138 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	139 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	140 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	141 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	142 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	143 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	144 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	145 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	146 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	147 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	148 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	149 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	150 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	151 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	152 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	153 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	154 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	155 <when value="BLOSUM45">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	156 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	157 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	158 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	159 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	160 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	161 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	162 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	163 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	164 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	165 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	166 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	167 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	168 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	169 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	170 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	171 <when value="PAM250">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	172 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	173 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	174 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	175 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	176 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	177 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	178 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	179 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	180 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	181 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	182 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	183 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	184 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	185 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	186 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	187 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	188 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	189 <when value="PAM70">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	190 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	191 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	192 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	193 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	194 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	195 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	196 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	197 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	198 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	199 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	200 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	201 <when value="PAM30">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	202 <param name="gap_costs" type="select" label="Gap Costs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	203 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	204 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	205 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	206 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	207 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	208 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	209 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	210 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	211 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	212 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	213 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	214 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	215 </conditional>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	216 </when>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	217 </conditional>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	218 <section name="annotation_options" expanded="false" title="Annotation Options">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	219 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	220 <option value="NOG">All organisms (NOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	221 <option value="aciNOG">Acidobacteria (aciNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	222 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	223 <option value="acoNOG">Aconoidasida (acoNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	224 <option value="actNOG">Actinobacteria (actNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	225 <option value="agaNOG">Agaricales (agaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	226 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	227 <option value="apiNOG">Apicomplexa (apiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	228 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	229 <option value="aquNOG">Aquificae (aquNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	230 <option value="arNOG">Archaea (arNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	231 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	232 <option value="artNOG">Arthropoda (artNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	233 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	234 <option value="ascNOG">Ascomycota (ascNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	235 <option value="aveNOG">Aves (aveNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	236 <option value="bacNOG">Bacilli (bacNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	237 <option value="bactNOG">Bacteria (bactNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	238 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	239 <option value="basNOG">Basidiomycota (basNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	240 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	241 <option value="biNOG">Bilateria (biNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	242 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	243 <option value="braNOG">Brassicales (braNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	244 <option value="carNOG">Carnivora (carNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	245 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	246 <option value="chlNOG">Chlorobi (chlNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	247 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	248 <option value="chloNOG">Chloroflexi (chloNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	249 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	250 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	251 <option value="chorNOG">Chordata (chorNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	252 <option value="chrNOG">Chromadorea (chrNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	253 <option value="cloNOG">Clostridia (cloNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	254 <option value="cocNOG">Coccidia (cocNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	255 <option value="creNOG">Crenarchaeota (creNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	256 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	257 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	258 <option value="cytNOG">Cytophagia (cytNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	259 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	260 <option value="defNOG">Deferribacteres (defNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	261 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	262 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	263 <option value="delNOG">delta/epsilon (delNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	264 <option value="dipNOG">Diptera (dipNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	265 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	266 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	267 <option value="droNOG">Drosophilidae (droNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	268 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	269 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	270 <option value="euNOG">Eukaryotes (euNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	271 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	272 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	273 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	274 <option value="fiNOG">Fishes (fiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	275 <option value="firmNOG">Firmicutes (firmNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	276 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	277 <option value="fuNOG">Fungi (fuNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	278 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	279 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	280 <option value="haeNOG">Haemosporida (haeNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	281 <option value="halNOG">Halobacteria (halNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	282 <option value="homNOG">Hominidae (homNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	283 <option value="hymNOG">Hymenoptera (hymNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	284 <option value="hypNOG">Hypocreales (hypNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	285 <option value="inNOG">Insects (inNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	286 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	287 <option value="lepNOG">Lepidoptera (lepNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	288 <option value="lilNOG">Liliopsida (lilNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	289 <option value="maNOG">Mammals (maNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	290 <option value="magNOG">Magnaporthales (magNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	291 <option value="meNOG">Animals (meNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	292 <option value="metNOG">Methanobacteria (metNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	293 <option value="methNOG">Methanococci (methNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	294 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	295 <option value="necNOG">Nectriaceae (necNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	296 <option value="negNOG">Negativicutes (negNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	297 <option value="nemNOG">Nematodes (nemNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	298 <option value="onyNOG">Onygenales (onyNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	299 <option value="opiNOG">Opisthokonts (opiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	300 <option value="perNOG">Peronosporales (perNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	301 <option value="plaNOG">Planctomycetes (plaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	302 <option value="pleNOG">Pleosporales (pleNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	303 <option value="poaNOG">Poales (poaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	304 <option value="prNOG">Primates (prNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	305 <option value="proNOG">Proteobacteria (proNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	306 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	307 <option value="roNOG">Rodents (roNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	308 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	309 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	310 <option value="sorNOG">Sordariales (sorNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	311 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	312 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	313 <option value="spiNOG">Spirochaetes (spiNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	314 <option value="spriNOG">Supraprimates (spriNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	315 <option value="strNOG">Streptophyta (strNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	316 <option value="synNOG">Synergistetes (synNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	317 <option value="tenNOG">Tenericutes (tenNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	318 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	319 <option value="theNOG">Thermoplasmata (theNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	320 <option value="therNOG">Thermotogae (therNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	321 <option value="thermNOG">Thermococci (thermNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	322 <option value="treNOG">Tremellales (treNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	323 <option value="veNOG">Vertebrates (veNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	324 <option value="verNOG">Verrucomicrobia (verNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	325 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	326 <option value="virNOG">Viridiplantae (virNOG)</option>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	327 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	335 <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	336 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	337 <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	338 <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	339 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	340 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	341 <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	342 <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	343 <help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	344 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	345 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	346 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	347 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	348 <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	349 <help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	350 Min bit score expected when searching for seed eggNOG ortholog.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	351 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	352 </help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	353 </param>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	354 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	355 <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	356 <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	357 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	358 <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	359 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	360 <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	361 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	362 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	363 </inputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	364 <outputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	365 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	366 <actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	367 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	368 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	369 </data>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	370 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	371 <filter>not output_options['no_annot']</filter>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	372 <actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	373 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG\|evalue\|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	374 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	375 </data>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	376 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	377 <filter>db['mode'] == 'hmmer'</filter>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	378 <actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	379 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	380 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	381 </data>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	382 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	383 <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	384 <actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	385 <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	386 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	387 </data>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	388 </outputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	389 <tests>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	390 <test>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	391 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	392 <param name="database" value="ENOG411CB2I"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	393 <param name="mode" value="hmmer"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	394 <param name="test" value="true"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	395 <param name="eggnog_data" value="eggNOG_4.5"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	396 <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	397 <param name="no_file_comments" value="true"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	398 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	399 </test>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	400 <test>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	401 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	402 <param name="eggnog_data" value="eggNOG_4.5"/> <!-- not passed in test, but required for test to work -->
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	403 <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	404 <param name="mode" value="diamond"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	405 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	406 </test>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	407 </tests>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	408 <help><![CDATA[
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	409
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	410 eggnog-mapper
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	411 =============
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	412 Overview
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	413 --------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	414
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	415 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	416 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	417 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	418 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	419
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	420 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	421
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	422 Options
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	423 -------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	424
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	425 ``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	426 HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	427
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	428
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	429 Outputs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	430 -------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	431
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	432 hmm_hits
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	433
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	434 For each query sequence, a list of significant
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	435 hits to eggNOG Orthologous Groups (OGs) is reported.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	436 Each line in the file represents a hit, where evalue, bit-score,
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	437 query-coverage and the sequence coordinates of the match are reported.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	438 If multiple hits exist for a given query, results are sorted by e-value.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	439 Only returned when using HMMER mode.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	440
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	441 seed_orthologs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	442
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	443 each line in the file provides the best match of each query within the best Orthologous Group (OG)
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	444 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	445 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	446 If using the diamond search mode, seed orthologs are directly
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	447 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	448
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	449 annotations
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	450
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	451 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	452
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	453 - ``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	454 - ``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	455 - ``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	456 - ``seed_ortholog_score``: best protein match (bit-score)
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	457 - ``predicted_gene_name``: Predicted gene name for query sequences
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	458 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	459 - ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	460 - ``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	461 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	462 - ``best_OG\|evalue\|score``: Best matching Orthologous Groups (only in HMM mode)
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	463 - ``COG functional categories``: COG functional category inferred from best matching OG
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	464 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	465
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	466 ]]></help>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	467 <citations>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	468 <citation type="doi">10.1093/nar/gkv1248</citation>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	469 </citations>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	470 </tool>

0

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="1.0.1">

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>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

3 <requirements>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

4 <requirement type="package" version="1.0.1">eggnog-mapper</requirement>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

5 </requirements>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

6 <version_command>emapper.py --version</version_command>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

7 <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

8 emapper.py

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

9 --data_dir '$eggnog_data.fields.db'

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

10 -m $db.mode

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

11 $translate

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

12 #if ($db.mode == 'hmmer'):

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

13 --database=$db.database.fields.db

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

14 #if $db.hmm_options.hmm_settings == 'specified':

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

15 --hmm_maxhits=$db.hmm_options.hmm_maxhits

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

16 --hmm_evalue=$db.hmm_options.hmm_evalue

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

17 --hmm_score=$db.hmm_options.hmm_score

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

18 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

19 #if str($db.hmm_options.hmm_qcov):

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

20 --hmm_qcov=$db.hmm_options.hmm_qcov

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

21 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

22 --Z=$db.hmm_options.Z

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

23 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

24 #elif ($db.mode == 'diamond'):

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

25 --matrix '$db.matrix_gapcosts.matrix'

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

26 $db.matrix_gapcosts.gap_costs

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

27 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

28 #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

29 --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

30 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

31 #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

32 --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

33 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

34 #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

35 --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

36 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

37 #if $seed_ortholog_options.seed_ortholog_evalue:

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

38 --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

39 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

40 #if str($seed_ortholog_options.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

41 --seed_ortholog_score=$seed_ortholog_options.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

42 #end if

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

43 $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

44 $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

45 $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

46 --output='results'

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

47 -i '${input}'

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

48 ]]></command>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

49 <inputs>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

50 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

51 <param name="eggnog_data" type="select" label="Version of eggNOG Database">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

52 <options from_data_table="eggnog_mapper">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

53 <filter type="static_value" name="type" value="data" column="2"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

54 </options>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

55 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

56 <param name="translate" type="boolean" truevalue="--translate" 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

57 label="Are these coding DNA sequences that need to be translated?"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

58 <conditional name="db">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

59 <param name="mode" type="select" label="Annotation Type">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

60 <option value="hmmer">HMM</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

61 <option value="diamond">DIAMOND</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

62 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

63 <when value="hmmer">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

64 <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed.">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

65 <options from_data_table="eggnog_mapper">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

66 <filter type="static_value" value="hmmer" column="2"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

67 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

68 </options>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

69 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

70 <conditional name="hmm_options">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

71 <param name="hmm_settings" type="select" label="HMM Search Options">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

72 <option value="default">Use defaults</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

73 <option value="specified">Set HMM Search Options</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

74 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

75 <when value="default"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

76 <when value="specified">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

77 <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

78 <param name="hmm_evalue" type="float" min="0" value="0.001" label="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

79 <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

80 <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" />

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

81 <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

82 <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" />

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

83 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

84 </conditional>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

85 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

86 <when value="diamond">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

87

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

88 <param name="database" type="hidden" value="diamond"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

89 <conditional name="matrix_gapcosts">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

90 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

91 <option value="BLOSUM90">BLOSUM90</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

92 <option value="BLOSUM80">BLOSUM80</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

93 <option value="BLOSUM62" selected="true">BLOSUM62</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

94 <option value="BLOSUM50">BLOSUM50</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

95 <option value="BLOSUM45">BLOSUM45</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

96 <option value="PAM250">PAM250</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

97 <option value="PAM70">PAM70</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

98 <option value="PAM30">PAM30</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

99 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

100 <when value="BLOSUM90">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

101 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

102 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

103 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

104 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

105 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

106 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

107 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

108 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

109 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

110 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

111 <when value="BLOSUM80">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

112 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

113 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

114 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

115 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

116 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

117 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

118 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

119 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

120 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

121 <when value="BLOSUM62">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

122 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

123 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

124 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

125 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

126 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

127 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

128 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

129 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

130 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

131 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

132 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

134 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

135 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

136 <when value="BLOSUM50">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

137 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

138 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

139 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

140 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

141 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

142 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

143 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

144 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

145 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

146 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

147 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

148 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

149 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

150 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

151 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

152 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

153 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

154 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

155 <when value="BLOSUM45">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

156 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

157 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

158 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

159 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

160 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

161 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

162 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

163 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

164 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

165 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

166 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

167 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

168 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

169 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

170 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

171 <when value="PAM250">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

172 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

173 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

174 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

175 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

176 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

177 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

178 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

179 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

180 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

181 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

182 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

183 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

184 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

185 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

186 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

187 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

188 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

189 <when value="PAM70">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

190 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

191 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

192 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

193 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

194 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

195 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

196 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

197 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

198 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

199 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

200 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

201 <when value="PAM30">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

202 <param name="gap_costs" type="select" label="Gap Costs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

203 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

204 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

205 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

206 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

207 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

208 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

209 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

210 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

211 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

212 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

213 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

214 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

215 </conditional>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

216 </when>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

217 </conditional>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

218 <section name="annotation_options" expanded="false" title="Annotation Options">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

219 <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

220 <option value="NOG">All organisms (NOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

221 <option value="aciNOG">Acidobacteria (aciNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

222 <option value="acidNOG">Acidobacteriia (acidNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

223 <option value="acoNOG">Aconoidasida (acoNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

224 <option value="actNOG">Actinobacteria (actNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

225 <option value="agaNOG">Agaricales (agaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

226 <option value="agarNOG">Agaricomycetes (agarNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

227 <option value="apiNOG">Apicomplexa (apiNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

228 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

229 <option value="aquNOG">Aquificae (aquNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

230 <option value="arNOG">Archaea (arNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

231 <option value="arcNOG">Archaeoglobi (arcNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

232 <option value="artNOG">Arthropoda (artNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

233 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

234 <option value="ascNOG">Ascomycota (ascNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

235 <option value="aveNOG">Aves (aveNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

236 <option value="bacNOG">Bacilli (bacNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

237 <option value="bactNOG">Bacteria (bactNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

238 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

239 <option value="basNOG">Basidiomycota (basNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

240 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

241 <option value="biNOG">Bilateria (biNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

242 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

243 <option value="braNOG">Brassicales (braNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

244 <option value="carNOG">Carnivora (carNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

245 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

246 <option value="chlNOG">Chlorobi (chlNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

247 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

248 <option value="chloNOG">Chloroflexi (chloNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

249 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

250 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

251 <option value="chorNOG">Chordata (chorNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

252 <option value="chrNOG">Chromadorea (chrNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

253 <option value="cloNOG">Clostridia (cloNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

254 <option value="cocNOG">Coccidia (cocNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

255 <option value="creNOG">Crenarchaeota (creNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

256 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

257 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

258 <option value="cytNOG">Cytophagia (cytNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

259 <option value="debNOG">Debaryomycetaceae (debNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

260 <option value="defNOG">Deferribacteres (defNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

261 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

262 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

263 <option value="delNOG">delta/epsilon (delNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

264 <option value="dipNOG">Diptera (dipNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

265 <option value="dotNOG">Dothideomycetes (dotNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

266 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

267 <option value="droNOG">Drosophilidae (droNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

268 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

269 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

270 <option value="euNOG">Eukaryotes (euNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

271 <option value="eurNOG">Euryarchaeota (eurNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

272 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

273 <option value="eurotNOG">Eurotiales (eurotNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

274 <option value="fiNOG">Fishes (fiNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

275 <option value="firmNOG">Firmicutes (firmNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

276 <option value="flaNOG">Flavobacteriia (flaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

277 <option value="fuNOG">Fungi (fuNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

278 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

279 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

280 <option value="haeNOG">Haemosporida (haeNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

281 <option value="halNOG">Halobacteria (halNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

282 <option value="homNOG">Hominidae (homNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

283 <option value="hymNOG">Hymenoptera (hymNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

284 <option value="hypNOG">Hypocreales (hypNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

285 <option value="inNOG">Insects (inNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

286 <option value="kinNOG">Kinetoplastida (kinNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

287 <option value="lepNOG">Lepidoptera (lepNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

288 <option value="lilNOG">Liliopsida (lilNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

289 <option value="maNOG">Mammals (maNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

290 <option value="magNOG">Magnaporthales (magNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

291 <option value="meNOG">Animals (meNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

292 <option value="metNOG">Methanobacteria (metNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

293 <option value="methNOG">Methanococci (methNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

294 <option value="methaNOG">Methanomicrobia (methaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

295 <option value="necNOG">Nectriaceae (necNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

296 <option value="negNOG">Negativicutes (negNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

297 <option value="nemNOG">Nematodes (nemNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

298 <option value="onyNOG">Onygenales (onyNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

299 <option value="opiNOG">Opisthokonts (opiNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

300 <option value="perNOG">Peronosporales (perNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

301 <option value="plaNOG">Planctomycetes (plaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

302 <option value="pleNOG">Pleosporales (pleNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

303 <option value="poaNOG">Poales (poaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

304 <option value="prNOG">Primates (prNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

305 <option value="proNOG">Proteobacteria (proNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

306 <option value="rhaNOG">Rhabditida (rhaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

307 <option value="roNOG">Rodents (roNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

308 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

309 <option value="saccNOG">Saccharomycetes (saccNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

310 <option value="sorNOG">Sordariales (sorNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

311 <option value="sordNOG">Sordariomycetes (sordNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

312 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

313 <option value="spiNOG">Spirochaetes (spiNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

314 <option value="spriNOG">Supraprimates (spriNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

315 <option value="strNOG">Streptophyta (strNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

316 <option value="synNOG">Synergistetes (synNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

317 <option value="tenNOG">Tenericutes (tenNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

318 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

319 <option value="theNOG">Thermoplasmata (theNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

320 <option value="therNOG">Thermotogae (therNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

321 <option value="thermNOG">Thermococci (thermNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

322 <option value="treNOG">Tremellales (treNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

323 <option value="veNOG">Vertebrates (veNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

324 <option value="verNOG">Verrucomicrobia (verNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

325 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

326 <option value="virNOG">Viridiplantae (virNOG)</option>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

327 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

328 <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

329 <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

330 <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

331 <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

332 <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

333 <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

334 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

335 <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

336 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

337 <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

338 <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

339 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

340 </section>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

341 <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

342 <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

343 <help>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

344 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

345 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

346 </help>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

347 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

348 <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

349 <help>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

350 Min bit score expected when searching for seed eggNOG ortholog.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

351 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

352 </help>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

353 </param>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

354 </section>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

355 <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

356 <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

357 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

358 <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

359 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

360 <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

361 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

362 </section>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

363 </inputs>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

364 <outputs>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

365 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

366 <actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

367 <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

368 </actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

369 </data>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

370 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

371 <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

372 <actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

373 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

374 </actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

375 </data>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

376 <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

377 <filter>db['mode'] == 'hmmer'</filter>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

378 <actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

379 <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

380 </actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

381 </data>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

382 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs" from_work_dir="results.emapper.annotations.orthologs">

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

383 <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

384 <actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

385 <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

386 </actions>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

387 </data>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

388 </outputs>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

389 <tests>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

390 <test>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

391 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

392 <param name="database" value="ENOG411CB2I"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

393 <param name="mode" value="hmmer"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

394 <param name="test" value="true"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

395 <param name="eggnog_data" value="eggNOG_4.5"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

396 <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

397 <param name="no_file_comments" value="true"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

398 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

399 </test>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

400 <test>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

401 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

402 <param name="eggnog_data" value="eggNOG_4.5"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

403 <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

404 <param name="mode" value="diamond"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

405 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

406 </test>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

407 </tests>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

408 <help><![CDATA[

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

409

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

410 eggnog-mapper

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

411 =============

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

412 Overview

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

413 --------

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

414

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

415 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

416 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

417 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

418 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

419

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

420 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

421

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

422 Options

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

423 -------

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

424

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

425 ``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

426 HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

427

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

428

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

429 Outputs

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

430 -------

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

431

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

432 **hmm_hits**

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

433

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

434 For each query sequence, a list of significant

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

435 hits to eggNOG Orthologous Groups (OGs) is reported.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

436 Each line in the file represents a hit, where evalue, bit-score,

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

437 query-coverage and the sequence coordinates of the match are reported.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

438 If multiple hits exist for a given query, results are sorted by e-value.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

439 Only returned when using HMMER mode.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

440

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

441 **seed_orthologs**

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

442

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

443 each line in the file provides the best match of each query within the best Orthologous Group (OG)

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

444 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

445 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

446 If using the diamond search mode, seed orthologs are directly

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

447 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

448

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

449 **annotations**

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

450

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

451 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

452

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

453 - ``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

454 - ``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

455 - ``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

456 - ``seed_ortholog_score``: best protein match (bit-score)

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

457 - ``predicted_gene_name``: Predicted gene name for query sequences

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

458 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

459 - ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

460 - ``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

461 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

462 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

463 - ``COG functional categories``: COG functional category inferred from best matching OG

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

464 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

465

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

466 ]]></help>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

467 <citations>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

468 <citation type="doi">10.1093/nar/gkv1248</citation>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

469 </citations>

f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f

galaxyp

parents:

diff changeset

470 </tool>

Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 0:f4e5279b5d10 draft