eggnog_mapper: eggnog_mapper.xml annotate

annotate eggnog_mapper.xml @ 12:9d1fbff733cf draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd

author	galaxyp
date	Tue, 19 Jul 2022 15:14:52 +0000
parents	5a30ae278db0
children	844fa988236b

rev	line source
11 5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 galaxyp parents: 10 diff changeset	1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	2 <description>functional sequence annotation by orthology</description>
4 2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99 galaxyp parents: 3 diff changeset	3 <macros>
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	4 <import>eggnog_macros.xml</import>
4 2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99 galaxyp parents: 3 diff changeset	5 </macros>
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	6 <expand macro="requirements"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	7 <expand macro="version_command"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	8 <command detect_errors="aggressive"><![CDATA[
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	9 #if $ortho_method.m == "no_search"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	10 cat
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	11 #for aht in $ortho_method.annotate_hits_table
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	12 $aht
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	13 #end for
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	14 > annotate_hits_table.tsv
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	15 &&
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	16 #end if
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	17
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	18 emapper.py
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	19 --data_dir '$eggnog_data.fields.path'
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	20 -m '$ortho_method.m'
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	21
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	22 #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	23 -i '$ortho_method.input'
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	24 --itype '$ortho_method.input_trans.itype'
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	25 #if $ortho_method.input_trans.itype in ['CDS', 'genome', 'metagenome']:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	26 $ortho_method.input_trans.translate
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	27 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	28 #if $ortho_method.input_trans.itype in ['genome', 'metagenome']:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	29 --genepred $ortho_method.input_trans.genepred
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	30 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	31 #elif $ortho_method.m == "no_search"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	32 --annotate_hits_table annotate_hits_table.tsv
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	33 #end if
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	34
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	35 #if $ortho_method.m == 'cache'
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	36 --cache '$ortho_method.cache'
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	37 #end if
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	38
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	39 #if $ortho_method.m in ['diamond', 'mmseqs']:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	40 ## Diamond option
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	41 #if $ortho_method.m == "diamond":
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	42 --matrix '$ortho_method.matrix_gapcosts.matrix'
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	43 $ortho_method.matrix_gapcosts.gap_costs
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	44 --sensmode $ortho_method.sensmode
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	45 $ortho_method.dmnd_iterate
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	46 $ortho_method.dmnd_ignore_warnings
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	47 #elif $ortho_method.m == "mmseqs":
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	48 --start_sens $ortho_method.start_sens
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	49 --sens_steps $ortho_method.sens_steps
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	50 --final_sens $ortho_method.final_sens
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	51 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	52
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	53 ## Common options for search filtering (applies to diamond and mmseqs only)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	54 #if str($ortho_method.query_cover):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	55 --query_cover $ortho_method.query_cover
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	56 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	57 #if str($ortho_method.subject_cover):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	58 --subject_cover $ortho_method.subject_cover
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	59 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	60 #if str($ortho_method.pident):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	61 --pident $ortho_method.pident
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	62 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	63 #if str($ortho_method.evalue):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	64 --evalue $ortho_method.evalue
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	65 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	66 #if str($ortho_method.score):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	67 --score $ortho_method.score
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	68 #end if
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	69 #end if
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	70
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	71 #if $annotation_options.no_annot == "--no_annot"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	72 --no_annot
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	73 #else
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	74 #if str($annotation_options.seed_ortholog_evalue):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	75 --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	76 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	77 #if str($annotation_options.seed_ortholog_score):
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	78 --seed_ortholog_score $annotation_options.seed_ortholog_score
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	79 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	80 #if $annotation_options.tax_scope:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	81 --tax_scope=$annotation_options.tax_scope
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	82 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	83 #if $annotation_options.target_orthologs:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	84 --target_orthologs=$annotation_options.target_orthologs
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	85 #end if
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	86 #if $annotation_options.go_evidence:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	87 --go_evidence=$annotation_options.go_evidence
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	88 #end if
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	89 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	90 $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	91 $output_options.report_orthologs
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	92 $output_options.md5
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	93 --output='results'
1 3c7c9396daaa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9505f2a447df1bcd46ceca7b5ddb532a2f8a1cd1 galaxyp parents: 0 diff changeset	94 --cpu "\${GALAXY_SLOTS:-4}"
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	95 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	96 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	97 ]]></command>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	98 <inputs>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	99 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
7 4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7" galaxyp parents: 6 diff changeset	100 <options from_data_table="eggnog_mapper_db_versioned">
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7" galaxyp parents: 6 diff changeset	101 <filter type="static_value" column="3" value="@IDX_VERSION@" />
4e4c6329f6cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7" galaxyp parents: 6 diff changeset	102 </options>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	103 </param>
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	104
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	105 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	106 <param argument="-m" type="select" label="Method to search seed orthologs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	107 <option value="diamond" selected="true">Diamond</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	108 <option value="mmseqs">MMseqs2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	109 <option value="no_search">Skip search stage: annotate an existing seed orthologs data set</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	110 <option value="cache">Skip search stage: annotate based on cached annotations (see also --md5)</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	111 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	112 <when value="diamond">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	113 <expand macro="fasta_input"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	114 <conditional name="matrix_gapcosts">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	115 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	116 <option value="BLOSUM90">BLOSUM90</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	117 <option value="BLOSUM80">BLOSUM80</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	118 <option value="BLOSUM62" selected="true">BLOSUM62</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	119 <option value="BLOSUM50">BLOSUM50</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	120 <option value="BLOSUM45">BLOSUM45</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	121 <option value="PAM250">PAM250</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	122 <option value="PAM70">PAM70</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	123 <option value="PAM30">PAM30</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	124 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	125 <when value="BLOSUM90">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	126 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	127 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	128 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	129 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	130 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	131 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	132 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	134 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	135 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	136 <when value="BLOSUM80">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	137 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	138 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	139 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	140 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	141 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	142 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	143 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	144 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	145 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	146 <when value="BLOSUM62">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	147 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	148 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	149 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	150 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	151 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	152 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	153 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	154 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	155 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	156 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	157 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	158 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	159 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	160 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	161 <when value="BLOSUM50">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	162 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	163 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	164 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	165 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	166 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	167 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	168 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	169 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	170 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	171 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	172 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	173 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	174 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	175 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	176 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	177 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	178 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	179 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	180 <when value="BLOSUM45">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	181 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	182 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	183 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	184 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	185 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	186 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	187 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	188 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	189 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	190 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	191 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	192 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	193 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	194 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	195 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	196 <when value="PAM250">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	197 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	198 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	199 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	200 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	201 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	202 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	203 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	204 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	205 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	206 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	207 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	208 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	209 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	210 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	211 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	212 </param>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	213 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	214 <when value="PAM70">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	215 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	216 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	217 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	218 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	219 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	220 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	221 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	222 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	223 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	224 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	225 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	226 <when value="PAM30">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	227 <param name="gap_costs" type="select" label="Gap Costs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	228 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	229 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	230 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	231 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	232 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	233 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	234 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	235 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	236 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	237 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	238 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	239 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	240 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	241 <param argument="--sensmode" type="select" label="Diamond's sensitivity mode">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	242 <option value="default">default</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	243 <option value="fast">fast</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	244 <option value="mid-sensitive">mid-sensitive</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	245 <option value="sensitive" selected="true">sensitive</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	246 <option value="more-sensitive">more-sensitive</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	247 <option value="very-sensitive">very-sensitive</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	248 <option value="ultra-sensitive">ultra-sensitive</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	249 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	250 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	251 label="Run diamond in iterative mode, up to the sensitivity level"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	252 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	253 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	254 <expand macro="common_search_options"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	255 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	256 <when value="mmseqs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	257 <expand macro="fasta_input"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	258 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	259 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	260 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	261 <expand macro="common_search_options"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	262 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	263 <when value="no_search">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	264 <param argument="--annotate_hits_table" type="data" multiple="true" format="tabular" label="Seed orthologs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	265 <validator type="expression" message="No seed orthologs">value.metadata.columns == 11</validator>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	266 <!-- would be cool to replace with this validator:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	267 <validator type="expression" message="No seed orthologs">value.metadata.column_names == '@SEED_ORTHOLOG_COLUMNS@'.split()</validator>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	268 but this does not work (yet) in tool tests since column_names can not be set in uploads -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	269 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	270 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	271 <when value="cache">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	272 <expand macro="fasta_input"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	273 <param argument="--cache" type="data" multiple="true" format="tabular" label="EggNOG Annotations with md5 hashes" help="Annotations computed with EggNOG mapper with enabled --md5 option">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	274 <validator type="expression" message="No seed orthologs">value.metadata.columns == 22</validator>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	275 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	276 <param name="output_no_annotations" type="boolean" checked="true" label="Output sequences without annotation" help="Produce an additional FASTA file with the sequences of queries for which an existing annotation was not found using cache mode. This file can be used as input of another eggNOG-mapper run without using the cache, trying to annotate the sequences."/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	277 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	278 </conditional>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	279
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	280 <conditional name="annotation_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	281 <param argument="--no_annot" type="select" label="Annotate seed orthologs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	282 <option value="">Yes</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	283 <option value="--no_annot">No</option>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	284 </param>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	285 <when value="">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	286 <param argument="--seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	287 <help>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	288 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	289 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	290 </help>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	291 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	292 <param argument="--seed_ortholog_score" type="float" optional="true" min="0" label="Minimum bit score threshold">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	293 <help>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	294 Min bit score expected when searching for seed eggNOG ortholog.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	295 Queries not having a significant seed orthologs will not be annotated.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	296 </help>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	297 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	298 <param argument="--tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	299 <param argument="--target_orthologs" type="select" label="target orthologs for functional transfer">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	300 <option value="one2one">one2one</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	301 <option value="many2one">many2one</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	302 <option value="one2many">one2many</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	303 <option value="many2many">many2many</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	304 <option value="all" selected="true">all</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	305 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	306 <param argument="--go_evidence" type="select"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	307 label="Select the set of GO terms that should be used for annotation">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	308 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	309 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	310 <option value="all" selected="true">All (experimental + non-electronic)</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	311 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	312 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	313 <when value="--no_annot"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	314 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	315
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	316 <section name="output_options" expanded="false" title="Output Options">
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	317 <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	318 label="Exclude header lines and stats from output files"/>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	319 <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	320 label="Output a file with the list of orthologs for each hits"/>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	321 <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	322 label="Add md5 hash of each query to annotations"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	323 </section>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	324 </inputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	325 <outputs>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	326 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	327 <filter>ortho_method['m'] not in ['no_search', 'cache']</filter>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	328 <actions>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	329 <action name="column_names" type="metadata" default="@SEED_ORTHOLOG_COLUMNS@"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	330 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	331 </data>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	332 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	333 <filter>annotation_options['no_annot'] == ''</filter>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	334 <actions>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	335 <conditional name="output_options.md5">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	336 <when value="True">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	337 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	338 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	339 <when value="False">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	340 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	341 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	342 </conditional>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	343 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	344 </data>
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	345 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	346 <filter>ortho_method['m'] != 'cache' and output_options['report_orthologs']</filter>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	347 <actions>
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	348 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	349 </actions>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	350 </data>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	351 <data name="no_annotations" format="fasta" label="${tool.name} on ${on_string}: Sequences wo annotation" from_work_dir="results.emapper.no_annotations.fasta">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	352 <filter>ortho_method['m'] == 'cache' and output_options['output_no_annotations']</filter>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	353 </data>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	354 </outputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	355 <tests>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	356 <!-- test producing only seed orthologs-->
11 5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 galaxyp parents: 10 diff changeset	357 <test expect_num_outputs="1">
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	358 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	359 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	360 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	361 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	362 <conditional name="annotation_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	363 <param name="no_annot" value="--no_annot"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	364 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	365 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	366 <param name="no_file_comments" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	367 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	368 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	369 <expand macro="stdout_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	370 </test>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	371
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	372 <!-- test producing annotations form seed orthologs -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	373 <test expect_num_outputs="2">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	374 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	375 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	376 <param name="m" value="no_search"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	377 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	378 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	379 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	380 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	381 <conditional name="annotation_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	382 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	383 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	384 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	385 <param name="no_file_comments" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	386 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	387 <expand macro="annotations_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	388 <expand macro="annotations_orthologs_assertion"/>
11 5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 galaxyp parents: 10 diff changeset	389 <expand macro="stdout_assertion"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	390 </test>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	391
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	392 <!-- test producing seed orthologs and annotations at once (ie the same as the previous two tests but in a single tool run) -->
11 5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 galaxyp parents: 10 diff changeset	393 <test expect_num_outputs="3">
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	394 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	395 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	396 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	397 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	398 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	399 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	400 <param name="no_file_comments" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	401 <param name="md5" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	402 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	403 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	404 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names=" md5" add_column_re="\t[\d\w]+"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	405 <expand macro="annotations_orthologs_assertion"/>
11 5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 galaxyp parents: 10 diff changeset	406 <expand macro="stdout_assertion"/>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	407 </test>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	408
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	409 <!-- test using chached annotations from previous run -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	410 <test expect_num_outputs="2">
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	411 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	412 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	413 <param name="m" value="cache"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	414 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	415 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	416 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	417 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	418 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	419 <param name="no_file_comments" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	420 <param name="md5" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	421 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	422 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names=" md5" add_column_re="\t[\d\w]+"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	423 <output name="no_annotations" ftype="fasta">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	424 <assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	425 <has_n_lines n="0"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	426 </assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	427 </output>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	428 <expand macro="stdout_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	429 </test>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	430
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	431 <!-- test setting tax scope-->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	432 <test expect_num_outputs="3">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	433 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	434 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	435 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	436 </conditional>
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	437 <section name="annotation_options">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	438 <param name="tax_scope" value="651137" />
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	439 </section>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	440 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	441 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	442 <param name="no_file_comments" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	443 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	444 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	445 <expand macro="annotations_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	446 <expand macro="annotations_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	447 <expand macro="stdout_assertion">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	448 <has_text text="--tax_scope=651137"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	449 </expand>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	450 </test>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	451
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	452 <!-- test setting a diamond option-->
11 5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2 galaxyp parents: 10 diff changeset	453 <test expect_num_outputs="3">
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	454 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	455 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	456 <param name="m" value="diamond" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	457 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	458 <param name="sensmode" value="fast" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	459 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	460 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	461 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	462 <param name="no_file_comments" value="true"/>
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	463 </section>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	464 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	465 <expand macro="annotations_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	466 <expand macro="annotations_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	467 <expand macro="stdout_assertion">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	468 <has_text text="--sensmode fast"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	469 </expand>
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	470 </test>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	471 <!-- not enabled as it requires a specific .db file, hard to minimize -->
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	472 <!--test>
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	473 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
8 96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	474 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	475 <section name="seed_ortho_options">
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	476 <conditional name="ortho_method">
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	477 <param name="m" value="mmseqs" />
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	478 <param name="start_sens" value="4" />
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	479 </conditional>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	480 </section>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	481 <param name="report_orthologs" value="true"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	482 <param name="no_file_comments" value="true"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	483 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	484 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	485 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66" galaxyp parents: 7 diff changeset	486 </test-->
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	487 </tests>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	488 <help><![CDATA[
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	489
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	490 eggnog-mapper
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	491 =============
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	492 Overview
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	493 --------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	494
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	495 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	496 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	497 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	498 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	499
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	500 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	501
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	502 Outputs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	503 -------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	504
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	505 seed_orthologs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	506
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	507 each line in the file provides the best match of each query within the best Orthologous Group (OG)
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	508 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	509 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	510 If using the diamond search mode, seed orthologs are directly
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	511 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	512
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	513 annotations
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	514
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	515 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	516
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	517 - ``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	518 - ``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	519 - ``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	520 - ``seed_ortholog_score``: best protein match (bit-score)
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	521 - ``predicted_taxonomic_group``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	522 - ``predicted_protein_name``: Predicted protein name for query sequences
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	523 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	524 - ``EC_number``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	525 - ``KEGG_KO``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	526 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	527 - ``KEGG_Module``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	528 - ``KEGG_Reaction``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	529 - ``KEGG_rclass``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	530 - ``BRITE``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	531 - ``KEGG_TC``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	532 - ``CAZy``
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	533 - ``BiGG_Reactions``
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	534 - ``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	535 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
6 3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	536 - ``best_OG\|evalue\|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	537 - ``COG_functional_categories``: COG functional category inferred from best matching OG
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5" galaxyp parents: 5 diff changeset	538 - ``eggNOG_free_text_description``
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	539
12 9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	540 Recommentation for large input data
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	541
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	542 EggNOG-mapper consists of two phases
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	543
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	544 1. finding seed orthologous sequences (compute intensive)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	545 2. expanding annotations (IO intensive)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	546
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	547 by default (i.e. if Method to search seed orthologs is not Skip search stage... and Annotate seed orthologs is Yes)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	548 both phases are executed within one tool run.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	549
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	550 For large input FASTA datasets in can be favourable to split this in two separate
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	551 tool runs as follows:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	552
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	553 1. Split the FASTA (e.g. 1M seqs per data set)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	554 2. Run the search phase only (set Annotate seed orthologs to No) on the separate FASTA files.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	555 3. Run the annotation phase (set Method to search seed orthologs to Skip search stage...)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	556
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	557 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	558
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	559 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	560
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd galaxyp parents: 11 diff changeset	561
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	562 ]]></help>
5 a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b" galaxyp parents: 4 diff changeset	563 <expand macro="citations"/>
0 f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f galaxyp parents: diff changeset	564 </tool>

Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 12:9d1fbff733cf draft