orthofinder_onlygroups: orthofinder_only

annotate orthofinder_only_groups.xml @ 5:974d8c28e586 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"

author	iuc
date	Mon, 17 Aug 2020 12:59:19 -0400
parents	999060f051ac
children	0ff17c7a18cd

rev	line source
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@">
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	2 <description>finds orthogroups in a set of proteomes</description>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	3 <macros>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	4 <import>macros.xml</import>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	5 </macros>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	6 <requirements>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
3 1aed170afb2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit c39323361ef6ba2664646e4476736c80bcd01124" iuc parents: 2 diff changeset	8 <requirement type="package" version="2.34">util-linux</requirement>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	9 </requirements>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	10 <command detect_errors="exit_code"><![CDATA[
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	11 #import re
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	12 ## prepare inputs
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	13 #if $init.start == "fasta":
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	14 #set $infiles = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	15 #for $input in $init.input_fasta
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	16 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	17 ln -s '$input' '${identifier}.fasta' &&
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	18 #set $infiles = $infiles + str($identifier) + ","
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	19 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	20 #set $infiles = $infiles[:-1]
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	21 #elif $init.start == "blast":
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	22 #set $infilesbl = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	23 #for $input in $init.input_blast_out
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	24 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	25 ln -s '$input' '$identifier' &&
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	26 #set $infilesbl = $infilesbl + str($identifier) + ","
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	27 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	28 #set $infilesbl = $infilesbl[:-1]
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	29
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	30 #set $infilesfa = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	31 #for $input in $init.input_blast_fa
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	32 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	33 ln -s '$input' '$identifier' &&
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	34 #set $infilesfa = $infilesfa + str($identifier) + ","
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	35 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	36 #set $infilesfa = $infilesfa[:-1]
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	37
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	38 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.specIDs.element_identifier))
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	39 ln -s $init.specIDs $identifier &&
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	40
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	41 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.seqIDs.element_identifier))
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	42 ln -s $init.seqIDs $identifier &&
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	43 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	44
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	45 ## start Orthofinder
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	46 orthofinder
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	47 #if $init.start == "fasta":
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	48 -f .
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	49 -S $init.search.search_program
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	50 #elif $init.start == "blast":
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	51 -b .
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	52 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	53
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	54 -I $I
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	55
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	56 #if $trees.run_mode == "full":
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	57 -M '${trees.tree_method.method}'
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	58 #if $trees.tree_method.method == "msa":
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	59 -A '${trees.tree_method.msa_program}'
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	60 -T '${trees.tree_method.msa_tree_program}'
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	61 #end if
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	62 #else:
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	63 $trees.run_mode
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	64 #end if
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	65
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	66 -t \${GALAXY_SLOTS:-1} -a \${GALAXY_SLOTS:-1} &&
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	67
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	68 mv OrthoFinder/Results_* results
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	69 #if $init.start == "fasta":
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	70 #if $init.search.search_program == "blast":
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	71 #if $init.search.keepblastout:
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	72 && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	73 mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	74 mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	75 #end if
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	76 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	77 #end if
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	78 ]]></command>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	79 <inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	80 <!-- Control where Orthofinder starts -->
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	81 <conditional name="init">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	82 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run.">
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	83 <option value="fasta" selected="true">From fasta proteomes</option>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	84 <option value="blast">From blast results</option>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	85 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	86
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	87 <when value="fasta">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	88 <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	89 <conditional name="search">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	90 <param name="search_program" type="select" label="Sequence search program">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	91 <option value="diamond" selected="true">Diamond (faster)</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	92 <option value="blast">Blast</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	93 <option value="blast_gz">Blast_gz - blast results gzipped</option>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	94 </param>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	95 <when value="blast">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	96 <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	97 </when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	98 <when value="diamond"></when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	99 <when value="blast_gz"></when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	100 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	101 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	102
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	103 <when value="blast">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	104 <param name="input_blast_out" type="data_collection" collection_type="list" format="txt" label="Select the pre-computed blast files" help="blastX_Y.txt files from the blast output files of a previous OrthoFinder run." />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	105 <param name="input_blast_fa" type="data_collection" collection_type="list" format="fasta" label="Select the fasta files" help="= SpeciesX.fa files from the blast output files of a previous OrthoFinder run." />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	106 <param name="specIDs" type="data" format="txt" label="Select the SpeciesIds file" help="SpeciesIDs.txt file from the blast output files of a previous OrthoFinder run."/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	107 <param name="seqIDs" type="data" format="txt" label="Select the SequencesIds file" help="SequencesIDs.txt file from the blast output files of a previous OrthoFinder run."/>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	108 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	109 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	110
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	111 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	112 <param name="run_mode" type="select" label="Orthofinder run mode">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	113 <option value="full" selected="true">Full run (including gene trees)</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	114 <option value="-og">Stop after inferring orthogroups (no gene trees)</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	115 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	116
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	117 <when value="full">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	118 <conditional name="tree_method">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	119 <param name="method" type="select" label="Method for gene tree inference">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	120 <option value="dendroblast" selected="true">Dendroblast (faster)</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	121 <option value="msa">MSA (Multiple Sequence Aligments)</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	122 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	123
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	124 <when value="msa">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	125 <param name="msa_program" type="select" label="MSA program">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	126 <option value="mafft" selected="true">Mafft</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	127 <option value="muscle">Muscle</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	128 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	129 <param name="msa_tree_program" type="select" label="Tree inference method">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	130 <option value="fasttree" selected="true">FastTree (recommended)</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	131 <option value="raxml">raxml</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	132 <option value="raxml-ng">raxml-ng</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	133 <option value="iqtree">iqtree</option>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	134 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	135 </when>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	136
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	137 <when value="dendroblast"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	138 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	139 </when>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	140
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	141 <when value="-og"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	142 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	143
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	144 <param argument="-I" type="float" value="1.5" label="Inflation parameter" help="Modify inflation parameter for MCL. Not recommended." />
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	145 <param name="output_duplications" type="boolean" checked="false" label="Generate output about gene duplication events"/>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	146 </inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	147 <outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	148 <!-- Orthogroups results -->
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	149 <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	150 <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	151 <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	152 <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	153 <data format="tsv" name="stat_overall" label="OrthoFinder on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	154 <data format="tsv" name="stat_specs" label="OrthoFinder on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv" />
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	155
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	156 <!-- working directory : blast outputs-->
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	157 <collection name="wdblast" type="list" label="OrthoFinder on ${on_string}: blast outputs">
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	158 <discover_datasets pattern="__name_and_ext__" directory="results/WorkingDirectory/blast" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	159 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	160 </collection>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	161 <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" >
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	162 <discover_datasets pattern="(?P<designation>.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	163 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	164 </collection>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	165 <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	166 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']"</filter>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	167 </data>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	168 <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	169 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	170 </data>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	171
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	172 <data format="newick" name="species_tree" label="OrthoFinder on ${on_string}: species tree" from_work_dir="results/Species_Tree/SpeciesTree_rooted.txt">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	173 <filter>trees['run_mode'] == "full"</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	174 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	175 <data format="newick" name="species_tree_label" label="OrthoFinder on ${on_string}: species tree with node labels" from_work_dir="results/Species_Tree/SpeciesTree_rooted_node_labels.txt">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	176 <filter>trees['run_mode'] == "full"</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	177 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	178 <collection name="genetrees" type="list" label="OrthoFinder on ${on_string}: gene trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	179 <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/Gene_Trees" format="newick" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	180 <filter>trees['run_mode'] == "full"</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	181 </collection>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	182
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	183 <data format="newick" name="species_tree_duplications" label="OrthoFinder on ${on_string}: species tree with duplication events" from_work_dir="results/Gene_Duplication_Events/SpeciesTree_Gene_Duplications_0.5_Support.txt">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	184 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	185 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	186 <data format="tsv" name="duplications" label="OrthoFinder on ${on_string}: duplication events" from_work_dir="results/Gene_Duplication_Events/Duplications.tsv">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	187 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	188 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	189 <data format="tsv" name="duplications_per_orthogroup" label="OrthoFinder on ${on_string}: duplications per orthogroup" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	190 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	191 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	192 <data format="tsv" name="duplications_per_species_tree_node" label="OrthoFinder on ${on_string}: duplications per species tree node" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	193 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	194 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	195 <collection name="resolved_trees" type="list" label="OrthoFinder on ${on_string}: resolved gene trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	196 <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/Resolved_Gene_Trees" format="newick" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	197 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	198 </collection>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	199 </outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	200 <tests>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	201 <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	202 <test>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	203 <conditional name="init">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	204 <param name="start" value="fasta" />
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	205 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	206 <conditional name="search">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	207 <param name="search_program" value="diamond"/>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	208 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	209 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	210 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	211 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	212 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	213 <param name="inflation" value="1.5" />
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	214 <output name="specs_overlap">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	215 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	216 <has_text text="AcAcaud_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	217 <has_text text="AmAmphi_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	218 <has_text text="ApApomp_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	219 <has_text text="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	220 <has_n_columns n="5"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	221 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	222 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	223 <output name="unassigned_genes">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	224 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	225 <has_text text="AcAcaud_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	226 <has_text text="AmAmphi_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	227 <has_text text="ApApomp_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	228 <has_text text="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	229 <has_n_columns n="5"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	230 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	231 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	232 <output name="stat_overall">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	233 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	234 <has_text text="Number of genes in orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	235 <has_text text="Number of unassigned genes"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	236 <has_text text="Percentage of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	237 <has_text text="Number of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	238 <has_text text="Number of genes"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	239 <has_text text="G50 (assigned genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	240 <has_text text="G50 (all genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	241 <has_text text="O50 (assigned genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	242 <has_text text="O50 (all genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	243 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	244 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	245 <output name="stat_specs">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	246 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	247 <has_text text="AcAcaud_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	248 <has_text text="AmAmphi_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	249 <has_text text="ApApomp_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	250 <has_text text="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	251 <has_text text="Number of genes per-species in orthogroup"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	252 <has_text text="Percentage of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	253 <has_text text="Number of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	254 <has_text text="Number of genes"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	255 <has_n_columns n="5"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	256 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	257 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	258 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	259 <!-- no trees + diamond + input files have extension fasta/faa/fa -->
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	260 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	261 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	262 <param name="start" value="fasta" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	263 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	264 <conditional name="search">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	265 <param name="search_program" value="diamond"/>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	266 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	267 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	268 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	269 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	270 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	271 <param name="inflation" value="1.5" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	272 <output name="specs_overlap">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	273 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	274 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	275 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	276 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	277 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	278 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	279 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	280 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	281 <output name="unassigned_genes">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	282 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	283 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	284 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	285 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	286 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	287 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	288 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	289 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	290 <output name="stat_overall">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	291 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	292 <has_text text="Number of genes in orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	293 <has_text text="Number of unassigned genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	294 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	295 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	296 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	297 <has_text text="G50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	298 <has_text text="G50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	299 <has_text text="O50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	300 <has_text text="O50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	301 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	302 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	303 <output name="stat_specs">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	304 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	305 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	306 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	307 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	308 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	309 <has_text text="Number of genes per-species in orthogroup"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	310 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	311 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	312 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	313 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	314 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	315 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	316 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	317 <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	318 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	319 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	320 <param name="start" value="fasta" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	321 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	322 <conditional name="search">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	323 <param name="search_program" value="blast"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	324 <param name="keepblastout" value="true" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	325 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	326 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	327 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	328 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	329 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	330 <param name="inflation" value="1.5" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	331 <output name="specs_overlap">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	332 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	333 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	334 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	335 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	336 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	337 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	338 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	339 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	340 <output name="unassigned_genes">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	341 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	342 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	343 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	344 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	345 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	346 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	347 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	348 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	349 <output name="stat_overall">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	350 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	351 <has_text text="Number of genes in orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	352 <has_text text="Number of unassigned genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	353 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	354 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	355 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	356 <has_text text="G50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	357 <has_text text="G50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	358 <has_text text="O50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	359 <has_text text="O50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	360 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	361 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	362 <output name="stat_specs">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	363 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	364 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	365 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	366 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	367 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	368 <has_text text="Number of genes per-species in orthogroup"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	369 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	370 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	371 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	372 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	373 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	374 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	375 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	376 <output_collection name="wdfasta" type="list" count="4"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	377 <output_collection name="wdblast" type="list" count="16"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	378 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	379 <!-- no trees + blast + input files have extension fasta/faa/fa-->
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	380 <test>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	381 <conditional name="init">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	382 <param name="start" value="fasta" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	383 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	384 <conditional name="search">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	385 <param name="search_program" value="blast"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	386 <param name="keepblastout" value="false" />
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	387 </conditional>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	388 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	389 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	390 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	391 </conditional>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	392 <param name="inflation" value="1.5" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	393 <output name="specs_overlap">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	394 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	395 <has_text text="Mycoplasma_agalactiae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	396 <has_text text="Mycoplasma_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	397 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	398 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	399 <has_n_columns n="5"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	400 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	401 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	402 <output name="unassigned_genes">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	403 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	404 <has_text text="Mycoplasma_agalactiae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	405 <has_text text="Mycoplasma_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	406 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	407 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	408 <has_n_columns n="5"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	409 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	410 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	411 <output name="stat_overall">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	412 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	413 <has_text text="Number of genes in orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	414 <has_text text="Number of unassigned genes"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	415 <has_text text="Percentage of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	416 <has_text text="Number of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	417 <has_text text="Number of genes"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	418 <has_text text="G50 (assigned genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	419 <has_text text="G50 (all genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	420 <has_text text="O50 (assigned genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	421 <has_text text="O50 (all genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	422 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	423 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	424 <output name="stat_specs">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	425 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	426 <has_text text="Mycoplasma_agalactiae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	427 <has_text text="Mycoplasma_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	428 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	429 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	430 <has_text text="Number of genes per-species in orthogroup"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	431 <has_text text="Percentage of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	432 <has_text text="Number of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	433 <has_text text="Number of genes"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	434 <has_n_columns n="5"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	435 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	436 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	437 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	438 <!-- no trees + uploaded blast-->
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	439 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	440 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	441 <param name="start" value="blast" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	442 <param name="input_blast_out">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	443 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	444 <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	445 <element name="Blast0_1.txt" value="inputs/blastout/Blast0_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	446 <element name="Blast0_2.txt" value="inputs/blastout/Blast0_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	447 <element name="Blast0_3.txt" value="inputs/blastout/Blast0_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	448 <element name="Blast1_0.txt" value="inputs/blastout/Blast1_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	449 <element name="Blast1_1.txt" value="inputs/blastout/Blast1_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	450 <element name="Blast1_2.txt" value="inputs/blastout/Blast1_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	451 <element name="Blast1_3.txt" value="inputs/blastout/Blast1_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	452 <element name="Blast2_0.txt" value="inputs/blastout/Blast2_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	453 <element name="Blast2_1.txt" value="inputs/blastout/Blast2_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	454 <element name="Blast2_2.txt" value="inputs/blastout/Blast2_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	455 <element name="Blast2_3.txt" value="inputs/blastout/Blast2_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	456 <element name="Blast3_0.txt" value="inputs/blastout/Blast3_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	457 <element name="Blast3_1.txt" value="inputs/blastout/Blast3_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	458 <element name="Blast3_2.txt" value="inputs/blastout/Blast3_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	459 <element name="Blast3_3.txt" value="inputs/blastout/Blast3_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	460 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	461 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	462 <param name="input_blast_fa">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	463 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	464 <element name="Species0.fa" value="inputs/blastfa/Species0.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	465 <element name="Species1.fa" value="inputs/blastfa/Species1.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	466 <element name="Species2.fa" value="inputs/blastfa/Species2.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	467 <element name="Species3.fa" value="inputs/blastfa/Species3.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	468 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	469 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	470 <param name="specIDs" ftype="txt" value="inputs/blastids/SpeciesIDs.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	471 <param name="seqIDs" ftype="txt" value="inputs/blastids/SequenceIDs.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	472 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	473 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	474 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	475 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	476 <param name="inflation" value="1.5" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	477 <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	478 <output name="orthogroups2" value="results_fromblast/Orthogroups.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	479 <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	480 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	481 <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	482 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	483 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	484 <!-- full mode + diamond + input files have extension fasta/faa/fa -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	485 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	486 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	487 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	488 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	489 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	490 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	491 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	492 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	493 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	494 <param name="run_mode" value="full" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	495 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	496 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	497 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	498 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	499 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	500 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	501 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	502 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	503 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	504 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	505 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	506 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	507 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	508 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	509 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	510 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	511 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	512 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	513 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	514 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	515 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	516 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	517 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	518 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	519 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	520 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	521 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	522 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	523 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	524 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	525 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	526 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	527 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	528 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	529 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	530 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	531 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	532 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	533 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	534 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	535 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	536 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	537 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	538 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	539 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	540 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	541 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	542 <output_collection name="genetrees" type="list" count="0"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	543 <output_collection name="resolved_trees" type="list" count="0"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	544 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	545 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	546 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	547 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	548 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	549 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	550 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	551 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	552 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	553 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	554 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	555 <param name="run_mode" value="full" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	556 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	557 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	558 <param name="output_duplications" value="true" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	559 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	560 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	561 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	562 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	563 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	564 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	565 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	566 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	567 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	568 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	569 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	570 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	571 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	572 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	573 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	574 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	575 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	576 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	577 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	578 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	579 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	580 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	581 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	582 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	583 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	584 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	585 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	586 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	587 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	588 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	589 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	590 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	591 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	592 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	593 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	594 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	595 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	596 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	597 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	598 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	599 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	600 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	601 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	602 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	603 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	604 <output name="species_tree_duplications" value="results/SpeciesTree_Gene_Duplications_0.5_Support.txt" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	605 <output name="duplications" value="results/Duplications.tsv" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	606 <output name="duplications_per_orthogroup" value="results/Duplications_per_Orthogroup.tsv" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	607 <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	608 <output_collection name="genetrees" type="list" count="325"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	609 <output_collection name="resolved_trees" type="list" count="325"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	610 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	611 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	612 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	613 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	614 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	615 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	616 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	617 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	618 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	619 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	620 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	621 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	622 <conditional name="tree_method">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	623 <param name="method" value="msa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	624 <param name="msa_program" value="muscle" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	625 <param name="msa_tree_program" value="raxml" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	626 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	627 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	628 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	629 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	630 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	631 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	632 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	633 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	634 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	635 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	636 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	637 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	638 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	639 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	640 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	641 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	642 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	643 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	644 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	645 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	646 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	647 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	648 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	649 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	650 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	651 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	652 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	653 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	654 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	655 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	656 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	657 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	658 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	659 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	660 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	661 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	662 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	663 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	664 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	665 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	666 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	667 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	668 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	669 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	670 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	671 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	672 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	673 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	674 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	675 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	676 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	677 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	678 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	679 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	680 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	681 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	682 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	683 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	684 <param name="run_mode" value="full" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	685 <conditional name="tree_method">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	686 <param name="method" value="msa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	687 <param name="msa_program" value="muscle" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	688 <param name="msa_tree_program" value="raxml" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	689 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	690 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	691 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	692 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	693 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	694 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	695 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	696 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	697 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	698 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	699 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	700 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	701 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	702 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	703 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	704 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	705 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	706 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	707 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	708 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	709 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	710 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	711 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	712 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	713 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	714 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	715 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	716 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	717 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	718 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	719 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	720 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	721 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	722 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	723 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	724 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	725 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	726 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	727 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	728 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	729 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	730 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	731 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	732 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	733 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	734 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	735 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	736 <assert_command>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	737 <has_text text="-M 'msa'"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	738 <has_text text="-A 'muscle'"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	739 <has_text text="-T 'raxml'"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	740 </assert_command>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	741 </test>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	742 </tests>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	743 <help>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	744 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	745 OrthoFinder OnlyGroups
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	746 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	747
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	748 Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md
3 1aed170afb2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit c39323361ef6ba2664646e4476736c80bcd01124" iuc parents: 2 diff changeset	749 Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	750
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	751 OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	752
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	753 .. class:: infomark
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	754
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	755 This galaxy tool implements the first part of the Orthofinder program, e.g. the clustering of orthogroups of genes.
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	756
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	757 If you have already ran OrthoFinder, the tool allows to re-run the analysis from the pre-computed blast-results.
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	758
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	759 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	760 Input files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	761 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	762 - When using "from fasta" option (e.g Orthofinder from scratch) : the input files are a set of proteomes in fasta format (on file per species). Choose this option if you have no OrthoFinder results yet.
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	763 - When using "from blast results" option : the input files are all the following files from of a previous OrthoFinder run (these files appear only if you have chosen to keep them while launching a previous run):
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	764 - A dataset collection / multiple datasets for the blast outputs
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	765 - A dataset collection / multiple datasets for .fa files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	766 - The SpeciesIDs.txt file
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	767 - The SequencesIDs.txt file
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	768
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	769 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	770 Parameters
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	771 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	772 - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster)
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	773 - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	774 - Inflation : the inflation parameter; modify this parameter is not recommended.
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	775
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	776 </help>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	777 <expand macro="citations"/>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	778 </tool>

Mercurial > repos > iuc > orthofinder_onlygroups

annotate orthofinder_only_groups.xml @ 5:974d8c28e586 draft