orthofinder_onlygroups: orthofinder_only

annotate orthofinder_only_groups.xml @ 7:904fb55e9156 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c"

author	iuc
date	Fri, 19 Nov 2021 10:29:04 +0000
parents	0ff17c7a18cd
children	3b974afde673

rev	line source
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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>
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	3 <xrefs>
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	4 <xref type="bio.tools">OrthoFinder</xref>
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	5 </xrefs>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	6 <macros>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	7 <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	8 </macros>
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 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	11 <requirement type="package" version="2.36">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	12 </requirements>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	13 <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	14 #import re
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	15 ## 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	16 #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	17 #set $infiles = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	18 #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	19 #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	20 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	21 #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	22 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	23 #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	24 #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	25 #set $infilesbl = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	26 #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	27 #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	28 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	29 #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	30 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	31 #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	32
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	33 #set $infilesfa = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	34 #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	35 #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	36 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	37 #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	38 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	39 #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	40
5 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.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	42 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	43
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	44 #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	45 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	46 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	47
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	48 ## start Orthofinder
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	49 orthofinder
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	50 #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	51 -f .
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	52 -S $init.search.search_program
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	53 $init.input_type
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	54 #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	55 -b .
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	56 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	57
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	58 -I $I
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	59
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	60 #if $trees.run_mode == "full":
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	61 -M '${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	62 #if $trees.tree_method.method == "msa":
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	63 -A '${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	64 -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	65 #end if
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	66 #else:
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	67 $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	68 #end if
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	69
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	70 -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	71
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	72 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	73 #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	74 #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	75 #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	76 && 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	77 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	78 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	79 #end if
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	80 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	81 #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	82 ]]></command>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	83 <inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	84 <!-- 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	85 <conditional name="init">
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	86 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta files' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run.">
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	87 <option value="fasta" selected="true">From fasta files</option>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	88 <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	89 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	90
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	91 <when value="fasta">
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	92 <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta files" help="One fasta file per species; species and sequence names in the results will remain the same than in the input files."/>
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	93 <param name="input_type" type="select" label="Input contains nucleotide or amino acid sequences?">
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	94 <option value="">Amino acid</option>
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	95 <option value="-d">Nucleotide</option>
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	96 </param>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	97 <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	98 <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	99 <option value="diamond" selected="true">Diamond (faster)</option>
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	100 <option value="diamond_ultra_sens">Diamond ultra-sensitive</option>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	101 <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	102 <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	103 </param>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	104 <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	105 <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	106 </when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	107 <when value="diamond"></when>
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	108 <when value="diamond_ultra_sens"></when>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	109 <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	110 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	111 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	112
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	113 <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	114 <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	115 <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	116 <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	117 <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	118 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	119 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	120
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	121 <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	122 <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	123 <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	124 <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	125 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	126
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	127 <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	128 <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	129 <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	130 <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	131 <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	132 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	133
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	134 <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	135 <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	136 <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	137 <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	138 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	139 <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	140 <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	141 <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	142 <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	143 <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	144 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	145 </when>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	146
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	147 <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	148 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	149 </when>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	150
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	151 <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	152 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	153
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	154 <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	155 <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	156 </inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	157 <outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	158 <!-- 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	159 <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	160 <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	161 <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	162 <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	163 <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	164 <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	165
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	166 <!-- 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	167 <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	168 <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	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 </collection>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	171 <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	172 <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	173 <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	174 </collection>
5 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="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	176 <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	177 </data>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	178 <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	179 <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	180 </data>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	181
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	182 <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	183 <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	184 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	185 <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	186 <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	187 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	188 <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	189 <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	190 <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	191 </collection>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	192
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	193 <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	194 <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	195 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	196 <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	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 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	199 <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	200 <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	201 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	202 <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	203 <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	204 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	205 <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	206 <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	207 <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	208 </collection>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	209 </outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	210 <tests>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	211 <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	212 <test expect_num_outputs="6">
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	213 <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	214 <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	215 <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	216 <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	217 <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	218 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	219 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	220 <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	221 <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	222 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	223 <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	224 <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	225 <assert_contents>
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="AcAcaud_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="AmAmphi_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="ApApomp_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_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	230 <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	231 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	232 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	233 <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	234 <assert_contents>
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="AcAcaud_trinity"/>
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="AmAmphi_trinity"/>
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="ApApomp_trinity"/>
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="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	239 <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	240 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	241 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	242 <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	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 <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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	254 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	255 <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	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 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	267 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	268 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	269 <!-- no trees + diamond + input files have extension fasta/faa/fa -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	270 <test expect_num_outputs="6">
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	271 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	272 <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	273 <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	274 <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	275 <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	276 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	277 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	278 <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	279 <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	280 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	281 <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	282 <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	283 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	287 <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	288 <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	289 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	290 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	291 <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	292 <assert_contents>
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	297 <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	298 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	299 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	300 <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	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 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	312 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	313 <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	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 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	325 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	326 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	327 <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	328 <test expect_num_outputs="10">
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	329 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	330 <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	331 <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	332 <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	333 <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	334 <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	335 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	336 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	337 <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	338 <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	339 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	340 <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	341 <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	342 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	346 <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	347 <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	348 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	349 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	350 <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	351 <assert_contents>
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	356 <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	357 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	358 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	359 <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	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 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	371 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	372 <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	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 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	384 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	385 <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	386 <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	387 <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	388 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	389 <!-- no trees + blast + input files have extension fasta/faa/fa-->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	390 <test expect_num_outputs="6">
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	391 <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	392 <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	393 <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	394 <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	395 <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	396 <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	397 </conditional>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	398 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	399 <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	400 <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	401 </conditional>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	402 <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	403 <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	404 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	408 <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	409 <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	410 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	411 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	412 <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	413 <assert_contents>
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	418 <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	419 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	420 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	421 <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	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 <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	424 <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	425 <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	426 <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	427 <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	428 <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	429 <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	430 <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	431 <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	432 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	433 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	434 <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	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 <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	437 <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	438 <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	439 <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	440 <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	441 <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	442 <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	443 <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	444 <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	445 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	446 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	447 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	448 <!-- no trees + uploaded blast-->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	449 <test expect_num_outputs="6">
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	450 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	451 <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	452 <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	453 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	454 <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	455 <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	456 <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	457 <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	458 <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	459 <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	460 <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	461 <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	462 <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	463 <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	464 <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	465 <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	466 <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	467 <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	468 <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	469 <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	470 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	471 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	472 <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	473 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	474 <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	475 <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	476 <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	477 <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	478 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	479 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	480 <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	481 <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	482 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	483 <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	484 <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	485 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	486 <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	487 <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	488 <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	489 <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	490 <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	491 <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	492 <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	493 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	494 <!-- full mode + diamond + input files have extension fasta/faa/fa -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	495 <test expect_num_outputs="9">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	496 <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	497 <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	498 <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	499 <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	500 <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	501 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	502 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	503 <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	504 <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	505 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	506 <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	507 <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	508 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	512 <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	513 <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	514 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	515 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	516 <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	517 <assert_contents>
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	522 <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	523 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	524 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	525 <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	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 <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	528 <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	529 <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	530 <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	531 <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	532 <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	533 <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	534 <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	535 <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	536 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	537 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	538 <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	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 <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	541 <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	542 <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	543 <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	544 <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	545 <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	546 <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	547 <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	548 <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	549 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	550 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	551 <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	552 <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	553 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	554 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	555 <test expect_num_outputs="14">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	556 <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	557 <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	558 <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	559 <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	560 <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	561 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	562 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	563 <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	564 <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	565 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	566 <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	567 <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	568 <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	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="unassigned_genes">
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	583 <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	584 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	585 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	586 <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	587 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	588 <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	589 <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	590 <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	591 <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	592 <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	593 <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	594 <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	595 <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	596 <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	597 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	598 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	599 <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	600 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	601 <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	602 <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	603 <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	604 <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	605 <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	606 <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	607 <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	608 <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	609 <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	610 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	611 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	612 <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	613 <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	614 <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	615 <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	616 <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	617 <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	618 <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	619 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	620 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	621 <test expect_num_outputs="6">
5 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="init">
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="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	624 <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	625 <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	626 <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	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 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	629 <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	630 <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	631 <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	632 <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	633 <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	634 <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	635 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	636 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	637 <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	638 <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	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="unassigned_genes">
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="AcAcaud_trinity"/>
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="AmAmphi_trinity"/>
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="ApApomp_trinity"/>
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="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	653 <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	654 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	655 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	656 <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	657 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	658 <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	659 <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	660 <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	661 <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	662 <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	663 <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	664 <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	665 <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	666 <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	667 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	668 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	669 <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	670 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	671 <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	672 <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	673 <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	674 <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	675 <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	676 <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	677 <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	678 <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	679 <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	680 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	681 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	682 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	683 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
6 0ff17c7a18cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 278a22cd0f7b47a958647e1e6dcf4bf56c4dcbbc" iuc parents: 5 diff changeset	684 <test expect_num_outputs="9">
5 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="init">
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="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	687 <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	688 <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	689 <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	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 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	692 <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	693 <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	694 <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	695 <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	696 <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	697 <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	698 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	699 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	700 <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	701 <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	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="unassigned_genes">
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	716 <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	717 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	718 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	719 <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	720 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	721 <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	722 <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	723 <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	724 <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	725 <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	726 <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	727 <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	728 <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	729 <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	730 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	731 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	732 <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	733 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	734 <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	735 <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	736 <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	737 <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	738 <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	739 <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	740 <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	741 <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	742 <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	743 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	744 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	745 <assert_command>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	746 <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	747 <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	748 <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	749 </assert_command>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	750 </test>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	751 </tests>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	752 <help>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	753 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	754 OrthoFinder OnlyGroups
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	755 ======================
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 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	758 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	759
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	760 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	761
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	762 .. class:: infomark
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	763
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	764 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	765
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	766 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	767
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	768 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	769 Input files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	770 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	771 - 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	772 - 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	773 - 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	774 - 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	775 - 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	776 - 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	777
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	778 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	779 Parameters
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	780 ----------
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	781 - Sequence search program : You can choose either blast, blast_gz, diamond, or diamond ultra-sensitive (diamond is faster)
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	782 - 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	783 - 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	784
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	785 </help>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	786 <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	787 </tool>

Mercurial > repos > iuc > orthofinder_onlygroups

annotate orthofinder_only_groups.xml @ 7:904fb55e9156 draft