orthofinder_onlygroups: orthofinder_only

annotate orthofinder_only_groups.xml @ 9:b3d25fae5389 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea

author	iuc
date	Mon, 15 Jan 2024 10:18:14 +0000
parents	3b974afde673
children

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>
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	3 <macros>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	4 <import>macros.xml</import>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	5 </macros>
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	6 <xrefs>
904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	7 <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	8 </xrefs>
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>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	11 </requirements>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	12 <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	13 #import re
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	14 ## 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	15 #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	16 #set $infiles = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	17 #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	18 #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	19 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	20 #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	21 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	22 #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	23 #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	24 #set $infilesbl = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	25 #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	26 #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	27 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	28 #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	29 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	30 #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	31
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	32 #set $infilesfa = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	33 #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	34 #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	35 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	36 #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	37 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	38 #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	39
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	40 #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	41 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	42
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	43 #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	44 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	45 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	46
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	47 ## start Orthofinder
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	48 orthofinder
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	49 #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	50 -f .
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	51 -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	52 $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	53 #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	54 -b .
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	55 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	56
8 3b974afde673 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 254941ef6bb2127fbcf2315e72f1361cd812c4b7" iuc parents: 7 diff changeset	57 -I $inflation
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	58
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	59 #if $trees.run_mode == "full":
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	60 -M '${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	61 #if $trees.tree_method.method == "msa":
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	62 -A '${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	63 -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	64 #end if
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	65 #else:
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	66 $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	67 #end if
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	68
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	69 -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	70
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	71 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	72 #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	73 #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	74 #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	75 && 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	76 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	77 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	78 #end if
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	79 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	80 #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	81 ]]></command>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	82 <inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	83 <!-- 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	84 <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	85 <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	86 <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	87 <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	88 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	89
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	90 <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	91 <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	92 <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	93 <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	94 <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	95 </param>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	96 <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	97 <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	98 <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	99 <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	100 <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	101 <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	102 </param>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	103 <when value="blast">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	104 <param name="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	105 </when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	106 <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	107 <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	108 <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	109 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	110 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	111
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	112 <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	113 <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	114 <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	115 <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	116 <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	117 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	118 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	119
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	120 <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	121 <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	122 <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	123 <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	124 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	125
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	126 <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	127 <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	128 <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	129 <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	130 <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	131 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	132
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	133 <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	134 <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	135 <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	136 <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	137 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	138 <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	139 <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	140 <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	141 <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	142 <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	143 </param>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	144 </when>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	145
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	146 <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	147 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	148 </when>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	149
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	150 <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	151 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	152
8 3b974afde673 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 254941ef6bb2127fbcf2315e72f1361cd812c4b7" iuc parents: 7 diff changeset	153 <param argument="-I" name="inflation" 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	154 <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	155 </inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	156 <outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	157 <!-- 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	158 <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	159 <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" />
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	160 <data format="tsv" name="hogs" label="OrthoFinder on ${on_string}: hierarchical orthogroups (tsv)" from_work_dir="results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv" >
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	161 <filter>trees['run_mode'] == "full"</filter>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	162 </data>
5 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="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	164 <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	165 <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	166 <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	167
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	168 <!-- 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	169 <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	170 <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	171 <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	172 </collection>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	173 <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	174 <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	175 <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	176 </collection>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	177 <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	178 <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	179 </data>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	180 <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	181 <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	182 </data>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	183
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	184 <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	185 <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	186 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	187 <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	188 <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	189 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	190 <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	191 <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	192 <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	193 </collection>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	194
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	195 <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	196 <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	197 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	198 <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	199 <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	200 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	201 <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	202 <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	203 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	204 <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	205 <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	206 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	207 <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	208 <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	209 <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	210 </collection>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	211 </outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	212 <tests>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	213 <!-- 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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	221 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	222 <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	223 <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	224 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	225 <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	226 <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	227 <assert_contents>
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="AcAcaud_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="AmAmphi_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_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	231 <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	232 <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	233 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	234 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	235 <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	236 <assert_contents>
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="AcAcaud_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="AmAmphi_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_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	240 <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	241 <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	242 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	243 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	244 <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	245 <assert_contents>
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="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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	256 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	257 <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	258 <assert_contents>
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="AcAcaud_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="AmAmphi_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="ApApomp_trinity"/>
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="AsAsp1_trinity"/>
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 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	264 <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	265 <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	266 <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	267 <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	268 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	269 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	270 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	271 <!-- 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	272 <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	273 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	274 <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	275 <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	276 <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	277 <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	278 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	279 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	280 <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	281 <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	282 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	283 <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	284 <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	285 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	288 <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	289 <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	290 <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	291 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	292 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	293 <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	294 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	297 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	298 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	299 <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	300 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	301 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	302 <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	303 <assert_contents>
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="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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	314 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	315 <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	316 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
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 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	322 <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	323 <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	324 <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	325 <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	326 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	327 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	328 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	329 <!-- 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	330 <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	331 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	332 <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	333 <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	334 <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	335 <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	336 <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	337 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	338 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	339 <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	340 <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	341 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	342 <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	343 <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	344 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	347 <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	348 <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	349 <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	350 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	351 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	352 <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	353 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	356 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	357 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	358 <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	359 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	360 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	361 <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	362 <assert_contents>
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="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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	373 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	374 <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	375 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
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 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	381 <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	382 <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	383 <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	384 <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	385 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	386 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	387 <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	388 <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	389 <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	390 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	391 <!-- 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	392 <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	393 <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	394 <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	395 <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	396 <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	397 <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	398 <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	399 </conditional>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	400 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	401 <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	402 <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	403 </conditional>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	404 <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	405 <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	406 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	409 <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	410 <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	411 <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	412 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	413 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	414 <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	415 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	418 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	419 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	420 <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	421 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	422 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	423 <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	424 <assert_contents>
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="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	426 <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	427 <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	428 <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	429 <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	430 <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	431 <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	432 <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	433 <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	434 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	435 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	436 <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	437 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
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 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	443 <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	444 <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	445 <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	446 <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	447 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	448 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	449 </test>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	450 <!-- 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	451 <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	452 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	453 <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	454 <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	455 <collection type="list">
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_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	457 <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	458 <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	459 <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	460 <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	461 <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	462 <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	463 <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	464 <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	465 <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	466 <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	467 <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	468 <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	469 <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	470 <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	471 <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	472 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	473 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	474 <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	475 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	476 <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	477 <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	478 <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	479 <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	480 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	481 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	482 <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	483 <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	484 </conditional>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	485 <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	486 <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	487 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	488 <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	489 <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	490 <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	491 <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	492 <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	493 <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	494 <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	495 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	496 <!-- full mode + diamond + input files have extension fasta/faa/fa -->
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	497 <test expect_num_outputs="10">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	498 <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	499 <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	500 <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	501 <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	502 <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	503 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	504 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	505 <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	506 <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	507 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	508 <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	509 <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	510 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	513 <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	514 <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	515 <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	516 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	517 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	518 <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	519 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	522 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	523 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	524 <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	525 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	526 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	527 <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	528 <assert_contents>
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="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	530 <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	531 <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	532 <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	533 <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	534 <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	535 <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	536 <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	537 <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	538 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	539 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	540 <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	541 <assert_contents>
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_agalactiae"/>
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_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
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 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	547 <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	548 <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	549 <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	550 <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	551 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	552 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	553 <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	554 <output_collection name="genetrees" type="list" count="0"/>
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	555 <output name="hogs">
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	556 <assert_contents>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	557 <has_text text="HOG" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	558 <has_text text="OG" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	559 <has_text text="Gene Tree Parent Clade" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	560 <has_text text="Mycoplasma_agalactiae"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	561 <has_text text="Mycoplasma_gallisepticum"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	562 <has_text text="Mycoplasma_genitalium"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	563 <has_text text="Mycoplasma_hyopneumoniae"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	564 <has_n_columns n="7"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	565 </assert_contents>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	566 </output>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	567 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	568 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	569 <test expect_num_outputs="15">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	570 <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	571 <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	572 <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	573 <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	574 <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	575 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	576 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	577 <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	578 <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	579 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	580 <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	581 <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	582 <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	583 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	584 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	585 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	586 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	587 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	588 <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	589 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	590 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	591 <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	592 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	593 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	594 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	595 <has_text text="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	597 <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	598 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	599 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	600 <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	601 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	602 <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	603 <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	604 <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	605 <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	606 <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	607 <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	608 <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	609 <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	610 <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	611 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	612 </output>
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="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	614 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	615 <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	616 <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	617 <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	618 <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	619 <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	620 <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	621 <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	622 <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	623 <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	624 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	625 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	626 <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	627 <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	628 <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	629 <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	630 <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	631 <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	632 <output_collection name="resolved_trees" type="list" count="325"/>
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	633 <output name="hogs">
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	634 <assert_contents>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	635 <has_text text="HOG" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	636 <has_text text="OG" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	637 <has_text text="Gene Tree Parent Clade" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	638 <has_text text="Mycoplasma_agalactiae"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	639 <has_text text="Mycoplasma_gallisepticum"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	640 <has_text text="Mycoplasma_genitalium"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	641 <has_text text="Mycoplasma_hyopneumoniae"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	642 <has_n_columns n="7"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	643 </assert_contents>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	644 </output>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	645 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	646 <!-- 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	647 <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	648 <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	649 <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	650 <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	651 <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	652 <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	653 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	654 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	655 <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	656 <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	657 <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	658 <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	659 <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	660 <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	661 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	662 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	663 <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	664 <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	665 <assert_contents>
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="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	667 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	668 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	669 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	670 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	671 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	672 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	673 <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	674 <assert_contents>
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="AcAcaud_trinity"/>
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="AmAmphi_trinity"/>
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="ApApomp_trinity"/>
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="AsAsp1_trinity"/>
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 <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	683 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	684 <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	685 <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	686 <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	687 <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	688 <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	689 <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	690 <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	691 <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	692 <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	693 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	694 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	695 <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	696 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	697 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	698 <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	699 <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	700 <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	701 <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	702 <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	703 <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	704 <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	705 <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	706 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	707 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	708 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	709 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	710 <test expect_num_outputs="10">
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	711 <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	712 <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	713 <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	714 <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	715 <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	716 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	717 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	718 <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	719 <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	720 <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	721 <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	722 <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	723 <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	724 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	725 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	726 <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	727 <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	728 <assert_contents>
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="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	730 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	731 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	732 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	733 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	734 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	735 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	736 <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	737 <assert_contents>
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="Mycoplasma_agalactiae"/>
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="Mycoplasma_gallisepticum"/>
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="Mycoplasma_genitalium"/>
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="Mycoplasma_hyopneumoniae"/>
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 <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	746 <assert_contents>
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="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	748 <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	749 <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	750 <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	751 <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	752 <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	753 <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	754 <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	755 <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	756 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	757 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	758 <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	759 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	760 <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	761 <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	762 <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	763 <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	764 <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	765 <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	766 <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	767 <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	768 <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	769 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	770 </output>
9 b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	771 <output name="hogs">
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	772 <assert_contents>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	773 <has_text text="HOG" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	774 <has_text text="OG" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	775 <has_text text="Gene Tree Parent Clade" />
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	776 <has_text text="Mycoplasma_agalactiae"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	777 <has_text text="Mycoplasma_gallisepticum"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	778 <has_text text="Mycoplasma_genitalium"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	779 <has_text text="Mycoplasma_hyopneumoniae"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	780 <has_n_columns n="7"/>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	781 </assert_contents>
b3d25fae5389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea iuc parents: 8 diff changeset	782 </output>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	783 <assert_command>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	784 <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	785 <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	786 <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	787 </assert_command>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	788 </test>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	789 </tests>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	790 <help>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	791 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	792 OrthoFinder OnlyGroups
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	793 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	794
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	795 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	796 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	797
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	798 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	799
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	800 .. class:: infomark
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	801
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	802 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	803
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	804 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	805
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	806 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	807 Input files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	808 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	809 - 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	810 - 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	811 - 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	812 - 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	813 - 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	814 - 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	815
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	816 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	817 Parameters
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	818 ----------
7 904fb55e9156 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c" iuc parents: 6 diff changeset	819 - 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	820 - 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	821 - 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	822
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	823 </help>
5 974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" iuc parents: 4 diff changeset	824 <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	825 </tool>

Mercurial > repos > iuc > orthofinder_onlygroups

annotate orthofinder_only_groups.xml @ 9:b3d25fae5389 draft default tip