annotate busco.xml @ 16:bb935709506a draft

planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
author iuc
date Thu, 12 Jan 2023 13:28:58 +0000
parents 41030a6c03b7
children e824f5d958d0
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 '${input}'
7
4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c"
iuc
parents: 6
diff changeset
33 --update-data
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
34 --mode '${busco_mode.mode}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
35 --out busco_galaxy
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
36 --cpu \${GALAXY_SLOTS:-4}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
37 --evalue ${adv.evalue}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
38 --limit ${adv.limit}
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
39
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
40 #if $lineage.lineage_mode == "auto_detect":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
41 $lineage.auto_lineage
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
42 #else if $lineage.lineage_mode == "select_lineage":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
43 --lineage_dataset '${lineage.lineage_dataset}'
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
44 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
45 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
46
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
47 ${busco_mode.use_augustus.long}
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
48 --augustus
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
49
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
50 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
51 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
52 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
53 --augustus_species local
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
54 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
55 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
56
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
57 #if $outputs and 'image' in $outputs:
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
58 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
59 mkdir BUSCO_summaries
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
60 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
61 ls -l busco_galaxy/run_*/ &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
62 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
63 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
64 generate_plot.py -wd BUSCO_summaries -rt specific
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
65 #end if
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
66
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
67 #if $outputs and 'gff' in $outputs:
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
68 &&
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
69 echo "\##gff-version 3" > busco_output.gff
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
70 &&
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
71 ## gff files can be absent
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
72 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
73 #end if
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
74
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
75 ]]> </command>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
76 <inputs>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
77 <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." />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
78 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
79 <param argument="--mode" type="select" label="Mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
80 <option value="geno">Genome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
81 <option value="tran">Transcriptome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
82 <option value="prot">annotated gene sets (protein)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
83 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
84 <when value="geno">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
85 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
86 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
87 <option value="yes">Yes, use Augustus</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
88 <option value="no" selected="true">Use Metaeuk</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
89 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
90 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
91 <when value="yes">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
92 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
93 <param name="augustus_mode" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
94 <option value="no" selected="true">Use the default species for selected lineage</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
95 <option value="builtin">Use another predefined species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
96 <option value="history">Use a custom species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
97 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
98 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
99 <when value="history">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
100 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
101 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
102 <when value="builtin">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
103 <param name="augustus_species" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
104 <expand macro="augustus_species" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
105 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
106 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
107 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
108 <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
109 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
110 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
111 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
112 <when value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
113 <when value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
114 </conditional>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
115
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
116 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
117 <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
118 <option value="auto_detect">Auto-detect</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
119 <option value="select_lineage">Select lineage</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
120 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
121 <when value="auto_detect">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
122 <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
123 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
124 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
125 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
126 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
127 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
128 <when value="select_lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
129 <param argument="--lineage_dataset" type="select" label="Lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
130 <expand macro="lineages" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
131 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
132 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
133 </conditional>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
134
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
135 <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
136 <option value="short_summary" selected="true">short summary text</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
137 <option value="missing">list with missing IDs</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
138 <option value="image">summary image</option>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
139 <option value="gff">gff</option>
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
140 </param>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
141
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
142 <section name="adv" title="Advanced Options" expanded="False">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
143 <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
144 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
145 </section>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
146 </inputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
147 <outputs>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
148 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
149 <filter>outputs and 'short_summary' in outputs</filter>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
150 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
151 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
152 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
153 <filter>outputs and 'missing' in outputs</filter>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
154 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
155 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
156 <filter>outputs and 'image' in outputs</filter>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
157 </data>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
158 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
159 <filter>outputs and 'gff' in outputs</filter>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
160 </data>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
161 </outputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
162 <tests>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
163 <test expect_num_outputs="4">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
164 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
165 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
166 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
167 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
168 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
169 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
170 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
171 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
172 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
173 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
174 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
175 <param name="outputs" value="short_summary,missing,gff" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
176 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
177 <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
178 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
179 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
180 <has_n_lines n="1"/>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
181 <has_text text="##gff-version 3" />
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
182 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
183 </output>
8
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
184 <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
185 <assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
186 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
187 </assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98"
iuc
parents: 7
diff changeset
188 </output>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
189 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
190 <test expect_num_outputs="5">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
191 <param name="input" value="proteome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
192 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
193 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
194 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
195 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
196 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
197 <param name="mode" value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
198 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
199 <param name="outputs" value="short_summary,missing,image,gff" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
200 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
201 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
202 <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
203 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
204 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
205 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
206 <has_n_lines n="1"/>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
207 <has_text text="##gff-version 3" />
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
208 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
209 </output>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
210 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
211 <test expect_num_outputs="5">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
212 <param name="input" value="transcriptome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
213 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
214 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
215 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
216 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
217 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
218 <param name="mode" value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
219 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
220 <param name="outputs" value="short_summary,missing,image,gff" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
221 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
222 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
223 <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
224 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
225 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
226 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
227 <test expect_num_outputs="3">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
228 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
229 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
230 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
231 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
232 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
233 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
234 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
235 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
236 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
237 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
238 <param name="augustus_mode" value="builtin" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
239 <param name="augustus_species" value="human" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
240 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
241 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
242 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
243 <param name="outputs" value="short_summary,gff" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
244 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
245 <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
246 <output name="busco_gff">
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
247 <assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
248 <has_n_lines n="1"/>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
249 <has_text text="##gff-version 3" />
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
250 </assert_contents>
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
251 </output>
2
382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 1
diff changeset
252 </test>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
253 <test expect_num_outputs="3">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
254 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
255 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
256 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
257 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
258 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
259 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
260 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
261 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
262 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
263 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
264 <param name="augustus_mode" value="history" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
265 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
266 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
267 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
268 </conditional>
13
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
iuc
parents: 12
diff changeset
269 <param name="outputs" value="short_summary,missing" />
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
270 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
271 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
272 <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
273 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
274 <test expect_num_outputs="5">
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
275 <param name="input" value="genome.fa" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
276 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
277 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
278 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
279 </conditional>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
280 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
281 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
282 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
283 <param name="use_augustus_selector" value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
284 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
285 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
286 <param name="outputs" value="short_summary,missing,image,gff" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
287 <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
288 <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
289 <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
290 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
291 <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
2
382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 1
diff changeset
292 </test>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
293 <test expect_num_outputs="5">
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
294 <param name="input" value="genome.fa" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
295 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
296 <param name="lineage_mode" value="auto_detect" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
297 <param name="auto_lineage" value="--auto-lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
298 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
299 <conditional name="busco_mode">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
300 <param name="mode" value="geno" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
301 <conditional name="use_augustus">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
302 <param name="use_augustus_selector" value="no" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
303 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
304 </conditional>
16
bb935709506a planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
iuc
parents: 15
diff changeset
305 <param name="outputs" value="short_summary,missing,image,gff" />
15
41030a6c03b7 "planemo upload commit 154d9b1916116b2880f34836d24a76129509086f"
iuc
parents: 13
diff changeset
306 <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
307 <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
308 <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
309 <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
310 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
12
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
iuc
parents: 11
diff changeset
311 </test>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
312 </tests>
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
313 <help><![CDATA[
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
314
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
315
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
316 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
317 --------------------------------------------------------------------------------------------------------------
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
318
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
319 Interpreting the results
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
320 ^^^^^^^^^^^^^^^^^^^^^^^^
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
321
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
322 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
323 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
324 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
325
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
326 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
327 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
328 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
329 (biological) or a chimeric assembly of haplotypes (technical).
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
330 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
331 Therefore you should filter them before a BUSCO analysis.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
332 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
333 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
334 is what you will be aiming for.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
335
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
336 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
337 .
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
338
4
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
iuc
parents: 3
diff changeset
339 .. _BUSCO: http://busco.ezlab.org/
9
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
340
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
341 ]]> </help>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
iuc
parents: 8
diff changeset
342 <expand macro="citations" />
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
343 </tool>