annotate busco.xml @ 19:2a5b8b9936bf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
author iuc
date Tue, 14 Nov 2023 13:03:37 +0000
parents 94170eee0ad8
children ea8146ee148f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
1 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
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
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
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 #else
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
44 --update-data
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
45 #end if
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
46
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
47 #if $lineage.lineage_mode == "auto_detect":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
48 $lineage.auto_lineage
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
49 #else if $lineage.lineage_mode == "select_lineage":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
50 --lineage_dataset '${lineage.lineage_dataset}'
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
51 #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
52
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
53 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
54
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
55 ${busco_mode.use_augustus.long}
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
56 --augustus
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
57
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
58 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
59 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
60 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
61 --augustus_species local
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
62 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
63 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
64
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
65 #if str( $busco_mode.mode ) == "geno":
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
66 #if $busco_mode.miniprot:
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
67 --miniprot
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
68 #end if
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
69 #end if
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
70
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
71 #if $outputs and 'image' in $outputs:
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
72 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
73 mkdir BUSCO_summaries
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
74 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
75 ls -l busco_galaxy/run_*/ &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
76 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
77 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
78 generate_plot.py -wd BUSCO_summaries -rt specific
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
79 #end if
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
80
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
81 #if $outputs and 'gff' in $outputs:
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
82 &&
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
83 echo "\##gff-version 3" > busco_output.gff
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
84 &&
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
85 ## gff files can be absent
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
86 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
87 #end if
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
88
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
89
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
90 ]]> </command>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
91 <inputs>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
92 <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
93 <conditional name="lineage_conditional">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
94 <param name="selector" type="select" label="Lineage data source">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
95 <option value="download">Download lineage data</option>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
96 <option value="cached">Use cached lineage data</option>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
97 </param>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
98 <when value="cached">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
99 <param name="cached_db" label="Cached database with lineage" type="select">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
100 <options from_data_table="busco_database">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
101 <validator message="No BUSCO database is available" type="no_options" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
102 </options>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
103 </param>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
104 </when>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
105 <when value="download"/>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
106 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
107 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
108 <param argument="--mode" type="select" label="Mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
109 <option value="geno">Genome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
110 <option value="tran">Transcriptome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
111 <option value="prot">annotated gene sets (protein)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
112 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
113 <when value="geno">
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
114 <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
115 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
116 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
117 <option value="yes">Yes, use Augustus</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
118 <option value="no" selected="true">Use Metaeuk</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
119 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
120 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
121 <when value="yes">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
122 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
123 <param name="augustus_mode" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
124 <option value="no" selected="true">Use the default species for selected lineage</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
125 <option value="builtin">Use another predefined species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
126 <option value="history">Use a custom species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
127 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
128 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
129 <when value="history">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
130 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
131 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
132 <when value="builtin">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
133 <param name="augustus_species" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
134 <expand macro="augustus_species" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
135 </param>
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 <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" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
139 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
140 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
141 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
142 <when value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
143 <when value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
144 </conditional>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
145
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
146 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
147 <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
148 <option value="auto_detect">Auto-detect</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
149 <option value="select_lineage">Select lineage</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
150 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
151 <when value="auto_detect">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
152 <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
153 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
154 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
155 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
156 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
157 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
158 <when value="select_lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
159 <param argument="--lineage_dataset" type="select" label="Lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
160 <expand macro="lineages" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
161 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
162 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
163 </conditional>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
164
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
165 <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
166 <option value="short_summary" selected="true">short summary text</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
167 <option value="missing">list with missing IDs</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
168 <option value="image">summary image</option>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
169 <option value="gff">gff</option>
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
170 </param>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
171
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
172 <section name="adv" title="Advanced Options" expanded="False">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
173 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
174 <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
175 <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
176 </section>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
177 </inputs>
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
178
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
179 <outputs>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
180 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
181 <filter>outputs and 'short_summary' in outputs</filter>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
182 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
183 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
184 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
185 <filter>outputs and 'missing' in outputs</filter>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
186 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
187 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
188 <filter>outputs and 'image' in outputs</filter>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
189 </data>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
190 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
191 <filter>outputs and 'gff' in outputs</filter>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
192 </data>
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
193 <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
194 <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
195 </data>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
196 </outputs>
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
197
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
198 <tests>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
199 <test expect_num_outputs="4">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
200 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
201 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
202 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
203 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
204 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
205 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
206 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
207 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
208 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
209 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
210 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
211 <param name="outputs" value="short_summary,missing,gff" />
17
e824f5d958d0 planemo upload commit 4b9a335c08b5d42b4297e641a28ff34b045810c3
iuc
parents: 16
diff changeset
212 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
213 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
214 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
215 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
216 <has_n_lines n="1"/>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
217 <has_text text="##gff-version 3" />
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
218 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
219 </output>
8
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
220 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
221 <assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
222 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
223 </assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
224 </output>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
225 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
226 <test expect_num_outputs="5">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
227 <param name="input" value="proteome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
228 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
229 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
230 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
231 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
232 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
233 <param name="mode" value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
234 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
235 <param name="outputs" value="short_summary,missing,image,gff" />
17
e824f5d958d0 planemo upload commit 4b9a335c08b5d42b4297e641a28ff34b045810c3
iuc
parents: 16
diff changeset
236 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
237 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
238 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
239 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
240 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
241 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
242 <has_n_lines n="1"/>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
243 <has_text text="##gff-version 3" />
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
244 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
245 </output>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
246 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
247 <test expect_num_outputs="5">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
248 <param name="input" value="transcriptome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
249 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
250 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
251 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
252 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
253 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
254 <param name="mode" value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
255 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
256 <param name="outputs" value="short_summary,missing,image,gff" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
257 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
258 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
259 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
260 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
261 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
262 </test>
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
263 <test expect_num_outputs="4">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
264 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
265 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
266 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
267 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
268 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
269 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
270 <param name="mode" value="geno" />
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
271 <param name="miniprot" value="true"/>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
272 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
273 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
274 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
275 <param name="augustus_mode" value="builtin" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
276 <param name="augustus_species" value="human" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
277 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
278 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
279 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
280 <param name="outputs" value="short_summary,gff" />
17
e824f5d958d0 planemo upload commit 4b9a335c08b5d42b4297e641a28ff34b045810c3
iuc
parents: 16
diff changeset
281 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
282 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
283 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
284 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
285 <has_n_lines n="1"/>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
286 <has_text text="##gff-version 3" />
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
287 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
288 </output>
19
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
289 <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
2a5b8b9936bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
iuc
parents: 18
diff changeset
290 <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
2
382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 1
diff changeset
291 </test>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
292 <test expect_num_outputs="3">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
293 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
294 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
295 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
296 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
297 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
298 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
299 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
300 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
301 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
302 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
303 <param name="augustus_mode" value="history" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
304 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
305 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
306 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
307 </conditional>
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
308 <param name="outputs" value="short_summary,missing" />
17
e824f5d958d0 planemo upload commit 4b9a335c08b5d42b4297e641a28ff34b045810c3
iuc
parents: 16
diff changeset
309 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
310 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
311 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
312 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
313 <test expect_num_outputs="5">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
314 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
315 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
316 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
317 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
318 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
319 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
320 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
321 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
322 <param name="use_augustus_selector" value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
323 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
324 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
325 <param name="outputs" value="short_summary,missing,image,gff" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
326 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
327 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
328 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
329 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
330 <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
2
382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 1
diff changeset
331 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
332 <test expect_num_outputs="5">
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
333 <param name="input" value="genome.fa" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
334 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
335 <param name="lineage_mode" value="auto_detect" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
336 <param name="auto_lineage" value="--auto-lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
337 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
338 <conditional name="busco_mode">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
339 <param name="mode" value="geno" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
340 <conditional name="use_augustus">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
341 <param name="use_augustus_selector" value="no" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
342 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
343 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
344 <param name="outputs" value="short_summary,missing,image,gff" />
15
41030a6c03b7 "planemo upload commit 154d9b1916116b2880f34836d24a76129509086f"
iuc
parents: 13
diff changeset
345 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
41030a6c03b7 "planemo upload commit 154d9b1916116b2880f34836d24a76129509086f"
iuc
parents: 13
diff changeset
346 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
41030a6c03b7 "planemo upload commit 154d9b1916116b2880f34836d24a76129509086f"
iuc
parents: 13
diff changeset
347 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
348 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
349 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
350 </test>
18
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
351 <test expect_num_outputs="2">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
352 <param name="input" value="genome.fa" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
353 <conditional name="lineage_conditional">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
354 <param name="selector" value="cached"/>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
355 <param name="cached_db" value="busco-demo-db-20230328"/>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
356 </conditional>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
357 <conditional name="lineage">
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
358 <param name="lineage_mode" value="select_lineage" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
359 <param name="lineage_dataset" value="archaea_odb10" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
360 </conditional>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
361 <param name="outputs" value="short_summary" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
362 <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
363 <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" />
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
364 <assert_stdout>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
365 <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
366 </assert_stdout>
94170eee0ad8 planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
iuc
parents: 17
diff changeset
367 </test>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
368 </tests>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
369 <help><![CDATA[
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
370
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
371
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
372 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
373 --------------------------------------------------------------------------------------------------------------
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
374
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
375 Interpreting the results
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
376 ^^^^^^^^^^^^^^^^^^^^^^^^
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
377
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
378 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
379 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
380 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
381
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
382 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
383 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
384 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
385 (biological) or a chimeric assembly of haplotypes (technical).
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
386 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
387 Therefore you should filter them before a BUSCO analysis.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
388 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
389 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
390 is what you will be aiming for.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
391
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
392 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
393 .
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
394
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
395 .. _BUSCO: http://busco.ezlab.org/
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
396
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
397 ]]> </help>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
398 <expand macro="citations" />
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
399 </tool>