busco: busco.xml annotate

annotate busco.xml @ 15:41030a6c03b7 draft

"planemo upload commit 154d9b1916116b2880f34836d24a76129509086f"

author	iuc
date	Mon, 11 Apr 2022 09:02:11 +0000
parents	46ae58b1d792
children	bb935709506a

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>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	3 <xrefs>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	4 <xref type="bio.tools">busco</xref>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	5 </xrefs>
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	6 <macros>
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	7 <import>macros.xml</import>
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	8 </macros>
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[
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	16 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	17 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	18 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
3 f18f0b887c31 planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b iuc parents: 2 diff changeset	19
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	20 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	21 ## Using an augustus model from history, we need to unzip it and let augustus find it
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	22 mkdir -p 'augustus_dir/species/' &&
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	23 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	24 #end if
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	25
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	26 busco
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	27 --in '${input}'
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	28 --update-data
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	29 --mode '${busco_mode.mode}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	30 --out busco_galaxy
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	31 --cpu \${GALAXY_SLOTS:-4}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	32 --evalue ${adv.evalue}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	33 --limit ${adv.limit}
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	34
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	35 #if $lineage.lineage_mode == "auto_detect":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	36 $lineage.auto_lineage
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	37 #else if $lineage.lineage_mode == "select_lineage":
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	38 --lineage_dataset '${lineage.lineage_dataset}'
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	39 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	40 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	41
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	42 ${busco_mode.use_augustus.long}
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	43 --augustus
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	44
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	45 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	46 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	47 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	48 --augustus_species local
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	49 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	50 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	51
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	52 #if $outputs and 'image' in $outputs:
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	53 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	54 mkdir BUSCO_summaries
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	55 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	56 ls -l busco_galaxy/run_*/ &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	57 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	58 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	59 generate_plot.py -wd BUSCO_summaries -rt specific
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	60 #end if
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	61
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	62 ]]> </command>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	63 <inputs>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	64 <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	65 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	66 <param argument="--mode" type="select" label="Mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	67 <option value="geno">Genome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	68 <option value="tran">Transcriptome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	69 <option value="prot">annotated gene sets (protein)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	70 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	71 <when value="geno">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	72 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	73 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	74 <option value="yes">Yes, use Augustus</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	75 <option value="no" selected="true">Use Metaeuk</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	76 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	77 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	78 <when value="yes">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	79 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	80 <param name="augustus_mode" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	81 <option value="no" selected="true">Use the default species for selected lineage</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	82 <option value="builtin">Use another predefined species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	83 <option value="history">Use a custom species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	84 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	85 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	86 <when value="history">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	87 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	88 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	89 <when value="builtin">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	90 <param name="augustus_species" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	91 <expand macro="augustus_species" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	92 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	93 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	94 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	95 <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	96 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	97 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	98 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	99 <when value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	100 <when value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	101 </conditional>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	102
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	103 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	104 <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	105 <option value="auto_detect">Auto-detect</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	106 <option value="select_lineage">Select lineage</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	107 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	108 <when value="auto_detect">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	109 <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	110 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	111 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	112 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	113 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	114 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	115 <when value="select_lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	116 <param argument="--lineage_dataset" type="select" label="Lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	117 <expand macro="lineages" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	118 </param>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	119 </when>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	120 </conditional>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	121
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	122 <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	123 <option value="short_summary" selected="true">short summary text</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	124 <option value="missing">list with missing IDs</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	125 <option value="image">summary image</option>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	126 </param>
46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	127
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	128 <section name="adv" title="Advanced Options" expanded="False">
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	129 <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	130 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	131 </section>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	132 </inputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	133 <outputs>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	134 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	135 <filter>outputs and 'short_summary' in outputs</filter>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	136 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	137 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	138 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	139 <filter>outputs and 'missing' in outputs</filter>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	140 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	141 <data name='summary_image' format='png' label="${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	142 <filter>outputs and 'image' in outputs</filter>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	143 </data>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	144 </outputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	145 <tests>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	146 <test expect_num_outputs="3">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	147 <param name="input" value="genome.fa" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	148 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	149 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	150 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	151 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	152 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	153 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	154 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	155 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	156 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	157 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	158 <param name="outputs" value="short_summary,missing" />
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	159 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	160 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
8 602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	161 <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	162 <assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	163 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	164 </assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	165 </output>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	166 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	167 <test expect_num_outputs="4">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	168 <param name="input" value="proteome.fa" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	169 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	170 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	171 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	172 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	173 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	174 <param name="mode" value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	175 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	176 <param name="outputs" value="short_summary,missing,image" />
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	177 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	178 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	179 <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	180 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	181 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	182 <test expect_num_outputs="4">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	183 <param name="input" value="transcriptome.fa" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	184 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	185 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	186 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	187 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	188 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	189 <param name="mode" value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	190 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	191 <param name="outputs" value="short_summary,missing,image" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	192 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	193 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	194 <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	195 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	196 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	197 <test expect_num_outputs="2">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	198 <param name="input" value="genome.fa" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	199 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	200 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	201 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	202 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	203 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	204 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	205 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	206 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	207 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	208 <param name="augustus_mode" value="builtin" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	209 <param name="augustus_species" value="human" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	210 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	211 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	212 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	213 <param name="outputs" value="short_summary" />
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	214 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	215 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	216 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	217 <test expect_num_outputs="3">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	218 <param name="input" value="genome.fa" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	219 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	220 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	221 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	222 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	223 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	224 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	225 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	226 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	227 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	228 <param name="augustus_mode" value="history" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	229 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	230 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	231 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	232 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	233 <param name="outputs" value="short_summary,missing" />
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	234 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	235 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	236 <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	237 </test>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	238 <test expect_num_outputs="4">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	239 <param name="input" value="genome.fa" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	240 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	241 <param name="lineage_mode" value="select_lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	242 <param name="lineage_dataset" value="arthropoda_odb10" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	243 </conditional>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	244 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	245 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	246 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	247 <param name="use_augustus_selector" value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	248 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	249 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	250 <param name="outputs" value="short_summary,missing,image" />
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	251 <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	252 <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	253 <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	254 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	255 </test>
12 1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	256 <test expect_num_outputs="4">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	257 <param name="input" value="genome.fa" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	258 <conditional name="lineage">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	259 <param name="lineage_mode" value="auto_detect" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	260 <param name="auto_lineage" value="--auto-lineage" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	261 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	262 <conditional name="busco_mode">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	263 <param name="mode" value="geno" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	264 <conditional name="use_augustus">
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	265 <param name="use_augustus_selector" value="no" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	266 </conditional>
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	267 </conditional>
13 46ae58b1d792 "planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" iuc parents: 12 diff changeset	268 <param name="outputs" value="short_summary,missing,image" />
15 41030a6c03b7 "planemo upload commit 154d9b1916116b2880f34836d24a76129509086f" iuc parents: 13 diff changeset	269 <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	270 <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	271 <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	272 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
1278204240d8 "planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19" iuc parents: 11 diff changeset	273 </test>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	274 </tests>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	275 <help><![CDATA[
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	276
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	277
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	278 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	279 --------------------------------------------------------------------------------------------------------------
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	280
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	281 Interpreting the results
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	282 ^^^^^^^^^^^^^^^^^^^^^^^^
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	283
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	284 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	285 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	286 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	287
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	288 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	289 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	290 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	291 (biological) or a chimeric assembly of haplotypes (technical).
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	292 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	293 Therefore you should filter them before a BUSCO analysis.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	294 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	295 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	296 is what you will be aiming for.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	297
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	298 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	299 .
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	300
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	301 .. _BUSCO: http://busco.ezlab.org/
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	302
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	303 ]]> </help>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	304 <expand macro="citations" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	305 </tool>

Mercurial > repos > iuc > busco

annotate busco.xml @ 15:41030a6c03b7 draft