busco: busco.xml annotate

annotate busco.xml @ 22:e5c372c91e46 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58

author	iuc
date	Tue, 29 Oct 2024 14:13:47 +0000
parents	2babe6d5c561
children

rev	line source
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	1 <tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	2 <description>Assess genome assembly and annotation completeness</description>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	3 <macros>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	4 <import>macros.xml</import>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	5 </macros>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	6 <xrefs>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	7 <xref type="bio.tools">busco</xref>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	8 </xrefs>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	9 <requirements>
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	10 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
11 0d243f458b53 "planemo upload commit cbeb631ec9f2f5d6af15693bc8453116b6776a4b" iuc parents: 9 diff changeset	11 <requirement type="package" version="1.34">tar</requirement>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	12 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	13 </requirements>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	14 <version_command>busco --version</version_command>
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	15 <command><![CDATA[
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	16
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'augustus':
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	18
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	19 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	20 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	21 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
3 f18f0b887c31 planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b iuc parents: 2 diff changeset	22
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	23 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	24 ## Using an augustus model from history, we need to unzip it and let augustus find it
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	25 mkdir -p 'augustus_dir/species/' &&
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	26 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	27 #end if
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	28
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	29 #end if
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	30
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	31 busco
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	32 --in '${input}'
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	33 --mode '${busco_mode.mode}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	34 --out busco_galaxy
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	35 --cpu \${GALAXY_SLOTS:-4}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	36 --evalue ${adv.evalue}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	37 --limit ${adv.limit}
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	38 --contig_break ${adv.contig_break}
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	39
18 94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	40 #if $lineage_conditional.selector == 'cached':
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	41 --offline
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	42 --download_path $lineage_conditional.cached_db.fields.path
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	43 #end if
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	44
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	45 #if $lineage.lineage_mode == "auto_detect":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	46 $lineage.auto_lineage
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	47 #else if $lineage.lineage_mode == "select_lineage":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	48 --lineage_dataset '${lineage.lineage_dataset}'
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	49 #end if
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	50
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	51 #if $busco_mode.mode == 'geno':
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	52 #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	53 --miniprot
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	54 #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	55 ${busco_mode.use_augustus.long}
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	56 --augustus
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	57 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	58 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	59 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	60 --augustus_species local
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	61 #end if
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	62 #else:
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	63 --metaeuk
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	64 #end if
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	65 #end if
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	66
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	67 #if $outputs and 'image' in $outputs:
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	68 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	69 mkdir BUSCO_summaries
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	70 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	71 ls -l busco_galaxy/run_*/ &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	72 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	73 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	74 generate_plot.py -wd BUSCO_summaries -rt specific
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	75 #end if
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	76
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	77 #if $outputs and 'gff' in $outputs:
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	78 &&
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	79 echo "\##gff-version 3" > busco_output.gff
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	80 &&
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	81 ## gff files can be absent
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	82 cat busco_galaxy/run_/busco_sequences/busco_sequences/*.gff >> busco_output.gff 2> /dev/null \|\| true
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	83 #end if
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	84
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	85
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	86 ]]></command>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	87 <inputs>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	88 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set."/>
18 94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	89 <conditional name="lineage_conditional">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	90 <param name="selector" type="select" label="Lineage data source">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	91 <option value="download">Download lineage data</option>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	92 <option value="cached">Use cached lineage data</option>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	93 </param>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	94 <when value="cached">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	95 <param name="cached_db" label="Cached database with lineage" type="select">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	96 <options from_data_table="busco_database">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	97 <validator message="No BUSCO database is available" type="no_options"/>
18 94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	98 </options>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	99 </param>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	100 </when>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	101 <when value="download"/>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	102 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	103 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	104 <param argument="--mode" type="select" label="Mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	105 <option value="geno">Genome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	106 <option value="tran">Transcriptome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	107 <option value="prot">annotated gene sets (protein)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	108 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	109 <when value="geno">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	110 <conditional name="use_augustus">
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	111 <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	112 <option value="augustus">Augustus</option>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	113 <option value="metaeuk">Metaeuk</option>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	114 <option value="miniprot" selected="true">Miniprot</option>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	115 </param>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	116 <when value="metaeuk"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	117 <when value="miniprot"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	118 <when value="augustus">
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	119 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	120 <param name="augustus_mode" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	121 <option value="no" selected="true">Use the default species for selected lineage</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	122 <option value="builtin">Use another predefined species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	123 <option value="history">Use a custom species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	124 </param>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	125 <when value="no"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	126 <when value="history">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	127 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	128 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	129 <when value="builtin">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	130 <param name="augustus_species" type="select" label="Augustus species model">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	131 <expand macro="augustus_species"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	132 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	133 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	134 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	135 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	136 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	137 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	138 </when>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	139 <when value="tran"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	140 <when value="prot"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	141 </conditional>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	142 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	143 <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	144 <option value="auto_detect">Auto-detect</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	145 <option value="select_lineage">Select lineage</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	146 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	147 <when value="auto_detect">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	148 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	149 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	150 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	151 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	152 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	153 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	154 <when value="select_lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	155 <param argument="--lineage_dataset" type="select" label="Lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	156 <expand macro="lineages"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	157 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	158 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	159 </conditional>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	160
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	161 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	162 <option value="short_summary" selected="true">short summary text</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	163 <option value="missing">list with missing IDs</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	164 <option value="image">summary image</option>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	165 <option value="gff">gff</option>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	166 </param>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	167
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	168 <section name="adv" title="Advanced Options" expanded="False">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	169 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches."/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	170 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	171 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	172 </section>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	173 </inputs>
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	174
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	175 <outputs>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	176 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	177 <filter>outputs and 'short_summary' in outputs</filter>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	178 </data>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	179 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	180 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	181 <filter>outputs and 'missing' in outputs</filter>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	182 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	183 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	184 <filter>outputs and 'image' in outputs</filter>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	185 </data>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	186 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	187 <filter>outputs and 'gff' in outputs</filter>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	188 </data>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	189 </outputs>
19 2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820 iuc parents: 18 diff changeset	190
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	191 <tests>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	192 <test expect_num_outputs="4">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	193 <param name="input" value="genome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	194 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	195 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	196 <param name="lineage_dataset" value="arthropoda_odb10"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	197 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	198 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	199 <param name="mode" value="geno"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	200 <conditional name="use_augustus">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	201 <param name="use_augustus_selector" value="augustus"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	202 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	203 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	204 <param name="outputs" value="short_summary,missing,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	205 <output name="busco_sum">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	206 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	207 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	208 <has_text text="Gene predictor used: augustus"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	209 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	210 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	211 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	212 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	213 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	214 <has_n_lines n="1"/>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	215 <has_text text="##gff-version 3"/>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	216 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	217 </output>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	218 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	219 </test>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	220 <test expect_num_outputs="5">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	221 <param name="input" value="proteome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	222 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	223 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	224 <param name="lineage_dataset" value="arthropoda_odb10"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	225 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	226 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	227 <param name="mode" value="prot"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	228 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	229 <param name="outputs" value="short_summary,missing,image,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	230 <output name="busco_sum">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	231 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	232 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	233 <has_text text="BUSCO was run in mode: proteins"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	234 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	235 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	236 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	237 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	238 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size"/>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	239 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	240 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	241 <has_n_lines n="1"/>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	242 <has_text text="##gff-version 3"/>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	243 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	244 </output>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	245 </test>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	246 <test expect_num_outputs="5">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	247 <param name="input" value="transcriptome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	248 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	249 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	250 <param name="lineage_dataset" value="arthropoda_odb10"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	251 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	252 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	253 <param name="mode" value="tran"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	254 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	255 <param name="outputs" value="short_summary,missing,image,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	256 <output name="busco_sum">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	257 <assert_contents>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	258 <has_text text="BUSCO was run in mode: euk_tran"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	259 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	260 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	261 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	262 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	263 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	264 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff"/>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	265 </test>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	266 <test expect_num_outputs="3">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	267 <param name="input" value="genome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	268 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	269 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	270 <param name="lineage_dataset" value="arthropoda_odb10"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	271 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	272 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	273 <param name="mode" value="geno"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	274 <conditional name="use_augustus">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	275 <param name="use_augustus_selector" value="augustus"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	276 <conditional name="aug_prediction">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	277 <param name="augustus_mode" value="builtin"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	278 <param name="augustus_species" value="human"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	279 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	280 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	281 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	282 <param name="outputs" value="short_summary,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	283 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	284 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	285 <has_text text="# Gene predictor used: augustus"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	286 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	287 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	288 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	289 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	290 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	291 <has_n_lines n="1"/>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	292 <has_text text="##gff-version 3"/>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	293 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	294 </output>
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	295 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	296 <test expect_num_outputs="3">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	297 <param name="input" value="genome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	298 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	299 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	300 <param name="lineage_dataset" value="arthropoda_odb10"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	301 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	302 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	303 <param name="mode" value="geno"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	304 <conditional name="use_augustus">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	305 <param name="use_augustus_selector" value="augustus"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	306 <conditional name="aug_prediction">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	307 <param name="augustus_mode" value="history"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	308 <param name="augustus_model" value="local.tar.gz" ftype="augustus"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	309 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	310 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	311 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	312 <param name="outputs" value="short_summary,missing"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	313 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	314 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	315 <has_text text="# Gene predictor used: augustus"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	316 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	317 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	318 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	319 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	320 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	321 </test>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	322 <test expect_num_outputs="5">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	323 <param name="input" value="genome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	324 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	325 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	326 <param name="lineage_dataset" value="arthropoda_odb10"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	327 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	328 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	329 <param name="mode" value="geno"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	330 <conditional name="use_augustus">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	331 <param name="use_augustus_selector" value="metaeuk"/>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	332 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	333 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	334 <param name="outputs" value="short_summary,missing,image,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	335 <output name="busco_sum">
20 ea8146ee148f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 9bf18dbcef34a48d3c40150ee953706bececfdd1 iuc parents: 19 diff changeset	336 <assert_contents>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	337 <has_text text="# Gene predictor used: metaeuk"/>
20 ea8146ee148f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 9bf18dbcef34a48d3c40150ee953706bececfdd1 iuc parents: 19 diff changeset	338 </assert_contents>
ea8146ee148f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 9bf18dbcef34a48d3c40150ee953706bececfdd1 iuc parents: 19 diff changeset	339 </output>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	340 <output name="busco_table" file="genome_results_metaeuk/full_table">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	341 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	342 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	343 <has_text text="9647at6656"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	344 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	345 </output>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	346 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	347 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	348 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	349 <has_text text="9647at6656"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	350 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	351 </output>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	352 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	353 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/>
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	354 </test>
16 bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe iuc parents: 15 diff changeset	355 <test expect_num_outputs="5">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	356 <param name="input" value="genome.fa"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	357 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	358 <param name="lineage_mode" value="auto_detect"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	359 <param name="auto_lineage" value="--auto-lineage"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	360 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	361 <conditional name="busco_mode">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	362 <param name="mode" value="geno"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	363 <conditional name="use_augustus">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	364 <param name="use_augustus_selector" value="metaeuk"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	365 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	366 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	367 <param name="outputs" value="short_summary,missing,image,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	368 <output name="busco_sum">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	369 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	370 <has_text text="Gene predictor used: metaeuk"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	371 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	372 </output>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	373 <output name="busco_table">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	374 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	375 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	376 <has_text text="The lineage dataset is: eukaryota_odb10"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	377 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	378 </output>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	379 <output name="busco_missing">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	380 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	381 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	382 <has_text text="The lineage dataset is: eukaryota_odb10"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	383 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	384 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	385 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	386 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff"/>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	387 </test>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	388 <test expect_num_outputs="3">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	389 <param name="input" value="genome.fa"/>
18 94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	390 <conditional name="lineage">
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	391 <param name="lineage_mode" value="select_lineage"/>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	392 <param name="lineage_dataset" value="arthropoda_odb10"/>
18 94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	393 </conditional>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	394 <param name="outputs" value="short_summary,gff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	395 <output name="busco_sum">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	396 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	397 <has_text text="# Gene predictor used: miniprot"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	398 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	399 </output>
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	400 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/>
21 2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	401 <output name="busco_table" file="genome_results_miniprot/full_table">
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	402 <assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	403 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	404 <has_text text="9647at6656"/>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	405 </assert_contents>
2babe6d5c561 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a iuc parents: 20 diff changeset	406 </output>
18 94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9 iuc parents: 17 diff changeset	407 </test>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	408 </tests>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	409 <help><![CDATA[
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	410
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	411
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	412 BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	413 --------------------------------------------------------------------------------------------------------------
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	414
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	415 Interpreting the results
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	416 ^^^^^^^^^^^^^^^^^^^^^^^^
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	417
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	418 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	419 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	420 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	421
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	422 BUSCO completeness results make sense only in the context of the biology of your organism.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	423 You have to understand whether missing or duplicated genes are of biological or technical origin.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	424 For instance, a high level of duplication may be explained by a recent whole duplication event
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	425 (biological) or a chimeric assembly of haplotypes (technical).
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	426 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	427 Therefore you should filter them before a BUSCO analysis.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	428 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	429 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	430 is what you will be aiming for.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	431
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	432 For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	433 .
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	434
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	435 .. _BUSCO: http://busco.ezlab.org/
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	436
22 e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	437 ]]></help>
e5c372c91e46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58 iuc parents: 21 diff changeset	438 <expand macro="citations"/>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	439 </tool>

Mercurial > repos > iuc > busco

annotate busco.xml @ 22:e5c372c91e46 draft default tip