orthofinder_onlygroups: orthofinder_only

annotate orthofinder_only_groups.xml @ 4:999060f051ac draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 39f97956b7cee2adee35aca2a19233dcda0c6b6d"

author	iuc
date	Wed, 13 May 2020 01:41:06 -0400
parents	1aed170afb2b
children	974d8c28e586

rev	line source
4 999060f051ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 39f97956b7cee2adee35aca2a19233dcda0c6b6d" iuc parents: 3 diff changeset	1 <tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="2.2.6">
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>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	3 <requirements>
4 999060f051ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 39f97956b7cee2adee35aca2a19233dcda0c6b6d" iuc parents: 3 diff changeset	4 <requirement type="package" version="2.2.6">orthofinder</requirement>
3 1aed170afb2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit c39323361ef6ba2664646e4476736c80bcd01124" iuc parents: 2 diff changeset	5 <requirement type="package" version="2.34">util-linux</requirement>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	6 </requirements>
3 1aed170afb2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit c39323361ef6ba2664646e4476736c80bcd01124" iuc parents: 2 diff changeset	7 <command detect_errors="exit_code">
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	8 <![CDATA[
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	9 ## 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	10 #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	11 #set $infiles = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	12 #for $input in $init.input_fasta
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	13 ln -s '$input' '${input.element_identifier}.fasta' &&
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	14 #set $infiles = $infiles + str($input.element_identifier) + ","
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	15 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	16 #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	17 #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	18 #set $infilesbl = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	19 #for $input in $init.input_blast_out
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	20 ln -s '$input' '$input.element_identifier' &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	21 #set $infilesbl = $infilesbl + str($input.element_identifier) + ","
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	22 #end for
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	23 #set $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	24
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	25 #set $infilesfa = ""
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	26 #for $input in $init.input_blast_fa
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	27 ln -s '$input' '$input.element_identifier' &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	28 #set $infilesfa = $infilesfa + str($input.element_identifier) + ","
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 $infilesfa = $infilesfa[:-1]
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	31
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	32 ln -s $init.specIDs $init.specIDs.element_identifier &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	33 ln -s $init.seqIDs $init.seqIDs.element_identifier &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	34 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	35
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	36 ## start Orthofinder
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	37 orthofinder
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	38 #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	39 -f .
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	40 -S $init.search.search_program
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	41 #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	42 -b .
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	43 #end if
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	44
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	45 -I $I -og -t \${GALAXY_SLOTS:-1} -a \${GALAXY_SLOTS:-1} &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	46
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	47 #if $init.start == "fasta":
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	48 mv 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	49 #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	50 #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	51 && 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	52 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	53 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	54 #end if
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	55 #end if
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	56 #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	57 mkdir results &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	58 mv *.csv results/ &&
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	59 mv Orthogroups.txt results/
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	60 #end if
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	61 ]]>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	62 </command>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	63 <inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	64 <!-- 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	65 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	66 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder_OnlyGroups works in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder_OnlyGroups from scratch and 'From blast results' if you have all the blast results from a previous OrthoFinder_OnlyGroups run.">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	67 <option value="fasta" selected="true">From fasta proteomes</option>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	68 <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	69 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	70
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	71 <when value="fasta">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	72 <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	73 <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	74 <param name="search_program" type="select" label="Sequence search program" help="Choose between blast, blast_gz, diamond">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	75 <option value="blast" selected="true">blast</option>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	76 <option value="blast_gz">blast_gz</option>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	77 <option value="diamond">diamond</option>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	78 </param>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	79 <when value="blast">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	80 <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder_OnlyGroups from pre-computed blast results"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	81 </when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	82 <when value="diamond"></when>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	83 <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	84 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	85 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	86
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	87 <when value="blast">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	88 <param name="input_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_OnlyGroups run." />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	89 <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_OnlyGroups run." />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	90 <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_OnlyGroups run."/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	91 <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_OnlyGroups run."/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	92 </when>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	93 </conditional>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	94 <param argument="-I" type="float" value="1.5" label="Inflation parameter" help="Modify inflation parameter for MCL. Not recommended." />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	95 </inputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	96 <outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	97 <!-- Orthogroups results -->
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	98 <data format="txt" name="orthogroups1" label="Orthogroups.txt" from_work_dir="results/Orthogroups.txt" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	99 <data format="csv" name="orthogroups2" label="Orthogroups.csv" from_work_dir="results/Orthogroups.csv" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	100 <data format="csv" name="specs_overlap" label="Orthogroups_SpeciesOverlaps.csv" from_work_dir="results/Orthogroups_SpeciesOverlaps.csv" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	101 <data format="csv" name="unassigned_genes" label="Orthogroups_UnassignedGenes.csv" from_work_dir="results/Orthogroups_UnassignedGenes.csv" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	102 <data format="csv" name="stat_overall" label="Statistics_Overall.csv" from_work_dir="results/Statistics_Overall.csv" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	103 <data format="csv" name="stat_specs" label="Statistics_PerSpecies.csv" from_work_dir="results/Statistics_PerSpecies.csv" />
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	104
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	105 <!-- working directory : blast outputs-->
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	106 <collection name="wdblast" type="list" label="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	107 <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	108 <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	109 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	110 <collection name="wdfasta" type="list" label="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	111 <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	112 <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	113 </collection>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	114 <collection name="genetrees" type="list" label="Gene trees">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	115 <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/WorkingDirectory/trees" format="nhx" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	116 <filter>dogenetrees</filter>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	117 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	118 <data format="txt" name="SpeciesIDs" label="SpeciesIDs.txt" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	119 <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	120 </data>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	121 <data format="txt" name="SequenceIDs" label="SequencesIDs.txt" 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	122 <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	123 </data>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	124 </outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	125 <tests>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	126 <!-- test orthofinder -f . -og when input files has no extension fasta/faa/fa ... -->
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	127 <test>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	128 <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	129 <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	130 <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	131 <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	132 <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	133 <param name="keepblastout" value="false" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	134 </conditional>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	135 </conditional>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	136 <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	137 <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	138 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	139 <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	140 <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	141 <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	142 <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	143 <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	144 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	145 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	146 <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	147 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	148 <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	149 <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	150 <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	151 <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	152 <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	153 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	154 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	155 <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	156 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	157 <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	158 <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	159 <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	160 <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	161 <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	162 <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	163 <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	164 <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	165 <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	166 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	167 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	168 <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	169 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	170 <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	171 <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	172 <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	173 <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	174 <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	175 <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	176 <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	177 <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	178 <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	179 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	180 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	181 </test>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	182 <!-- test orthofinder -f -og -->
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	183 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	184 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	185 <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	186 <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	187 <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	188 <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	189 <param name="keepblastout" value="false" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	190 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	191 </conditional>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	192 <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	193 <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	194 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	195 <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	196 <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	197 <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	198 <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	199 <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	200 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	201 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	202 <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	203 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	204 <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	205 <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	206 <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	207 <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	208 <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	209 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	210 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	211 <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	212 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221 <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	222 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	223 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	224 <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	225 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	226 <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	227 <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	228 <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	229 <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	230 <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	231 <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	232 <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	233 <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	234 <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	235 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	236 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	237 </test>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	238
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	239 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	240 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	241 <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	242 <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	243 <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	244 <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	245 <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	246 </conditional>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	247 </conditional>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	248 <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	249 <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	250 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	251 <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	252 <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	253 <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	254 <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	255 <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	256 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	257 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	258 <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	259 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	260 <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	261 <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	262 <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	263 <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	264 <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	265 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	266 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	267 <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	268 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	279 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	280 <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	281 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	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="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	294 <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	295 <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	296 </test>
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	297
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	298 <!-- test -S diamond -->
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	299 <test>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	300 <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	301 <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	302 <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	303 <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	304 <param name="search_program" value="diamond"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	305 </conditional>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	306 </conditional>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	307 <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	308 <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	309 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	310 <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	311 <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	312 <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	313 <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	314 <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	315 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	316 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	317 <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	318 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	319 <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	320 <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	321 <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	322 <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	323 <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	324 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	325 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	326 <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	327 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	338 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	339 <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	340 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 <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	348 <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	349 <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	350 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	351 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	352 </test>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	353
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	354 <!-- test orthofinder -b -og -->
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	355 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	356 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	357 <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	358 <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	359 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <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	373 <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	374 <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	375 <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	376 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	377 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	378 <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	379 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	380 <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	381 <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	382 <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	383 <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	384 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	385 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	386 <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	387 <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	388 </conditional>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	389 <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	390 <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	391 <output name="orthogroups2" value="results_fromblast/Orthogroups.csv"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	392 <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	393 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	394 <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	395 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	396 </test>
1 918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca iuc parents: 0 diff changeset	397 </tests>
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	398 <help>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	399 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	400 OrthoFinder OnlyGroups
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	401 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	402
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	403 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	404 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	405
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	406 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	407
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	408 .. class:: infomark
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	409
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	410 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	411
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	412 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	413
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	414 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	415 Input files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	416 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	417 - 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	418 - 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	419 - 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	420 - 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	421 - 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	422 - 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	423
2 649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	424 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	425 Parameters
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	426 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	427 - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster)
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840 iuc parents: 1 diff changeset	428 - 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	429 - 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	430
0 bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	431 </help>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	432 <citations>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	433 <citation type="doi">10.1186/s13059-015-0721-2</citation>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	434 </citations>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f iuc parents: diff changeset	435 </tool>

Mercurial > repos > iuc > orthofinder_onlygroups

annotate orthofinder_only_groups.xml @ 4:999060f051ac draft