busco: busco.xml annotate

annotate busco.xml @ 11:0d243f458b53 draft

"planemo upload commit cbeb631ec9f2f5d6af15693bc8453116b6776a4b"

author	iuc
date	Mon, 26 Jul 2021 21:29:40 +0000
parents	cf13a1e03e5b
children	1278204240d8

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>
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	3 <macros>
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	4 <import>macros.xml</import>
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	5 </macros>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	6 <requirements>
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
11 0d243f458b53 "planemo upload commit cbeb631ec9f2f5d6af15693bc8453116b6776a4b" iuc parents: 9 diff changeset	8 <requirement type="package" version="1.34">tar</requirement>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	9 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	10 </requirements>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	11 <version_command>busco --version</version_command>
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	12 <command><![CDATA[
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	13 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	14 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	15 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
3 f18f0b887c31 planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b iuc parents: 2 diff changeset	16
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	18 ## Using an augustus model from history, we need to unzip it and let augustus find it
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	19 mkdir -p 'augustus_dir/species/' &&
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	20 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	21 #end if
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	22
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	23 busco
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	24 --in '${input}'
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	25 --lineage_dataset '${lineage_dataset}'
4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	26 --update-data
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	27 --mode '${busco_mode.mode}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	28 --out busco_galaxy
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	29 --cpu \${GALAXY_SLOTS:-4}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	30 --evalue ${adv.evalue}
5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	31 --limit ${adv.limit}
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	32
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	33 #if $adv.auto_lineage:
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	34 $adv.auto_lineage
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	35 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	36 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	37
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	38 ${busco_mode.use_augustus.long}
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	39 --augustus
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	40
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	41 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	42 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	43 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	44 --augustus_species local
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	45 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	46 #end if
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	47
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	48 #if $adv.outputs and 'image' in $adv.outputs:
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	49 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	50 mkdir BUSCO_summaries
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	51 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	52 ls -l busco_galaxy/run_*/ &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	53 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	54 &&
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	55 generate_plot.py -wd BUSCO_summaries -rt specific
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	56 #end if
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	57
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	58 ]]> </command>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	59 <inputs>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	60 <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	61 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	62 <param argument="--mode" type="select" label="Mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	63 <option value="geno">Genome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	64 <option value="tran">Transcriptome assemblies (DNA)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	65 <option value="prot">annotated gene sets (protein)</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	66 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	67 <when value="geno">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	68 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	69 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	70 <option value="yes">Yes, use Augustus</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	71 <option value="no" selected="true">Use Metaeuk</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	72 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	73 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	74 <when value="yes">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	75 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	76 <param name="augustus_mode" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	77 <option value="no" selected="true">Use the default species for selected lineage</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	78 <option value="builtin">Use another predefined species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	79 <option value="history">Use a custom species model</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	80 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	81 <when value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	82 <when value="history">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	83 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	84 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	85 <when value="builtin">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	86 <param name="augustus_species" type="select" label="Augustus species model">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	87 <expand macro="augustus_species" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	88 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	89 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	90 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	91 <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	92 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	93 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	94 </when>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	95 <when value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	96 <when value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	97 </conditional>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	98
7 4048d82f0c88 "planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" iuc parents: 6 diff changeset	99 <param argument="--lineage_dataset" type="select" label="Lineage">
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	100 <expand macro="lineages" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	101 </param>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	102
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	103 <section name="adv" title="Advanced Options" expanded="False">
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	104 <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	105 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	106 <param name="auto_lineage" type="select" optional="true" label="Run auto-lineage to find optimal lineage path">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	107 <option value="--auto-lineage">Run auto-lineage to find optimum lineage path</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	108 <option value="--auto-lineage-prok">Run auto-lineage just on non-eukaryote trees to find optimum lineage path</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	109 <option value="--auto-lineage-euk">Run auto-placement just on eukaryote tree to find optimum lineage path</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	110 </param>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	111 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	112 <option value="short_summary">short summary text</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	113 <option value="missing">list with missing IDs</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	114 <option value="image">summary image</option>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	115 </param>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	116 </section>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	117 </inputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	118 <outputs>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	119 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	120 <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	121 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	122 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	123 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	124 <filter>adv['outputs'] and 'missing' in adv['outputs']</filter>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	125 </data>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	126 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	127 <filter>adv['outputs'] and 'image' in adv['outputs']</filter>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	128 </data>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	129 </outputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	130 <tests>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	131 <test expect_num_outputs="3">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	132 <param name="input" value="genome.fa" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	133 <param name="lineage_dataset" value="arthropoda_odb10" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	134 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	135 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	136 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	137 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	138 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	139 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	140 <section name="adv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	141 <param name="outputs" value="short_summary,missing" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	142 </section>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	143 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	144 <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	145 <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	146 <assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	147 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	148 </assert_contents>
602fb8e63aa7 "planemo upload commit 92185cd605fe0cfa78593ea10b0222e8aeb6ef98" iuc parents: 7 diff changeset	149 </output>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	150 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	151 <test expect_num_outputs="4">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	152 <param name="input" value="proteome.fa" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	153 <param name="lineage_dataset" value="arthropoda_odb10" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	154 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	155 <param name="mode" value="prot" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	156 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	157 <section name="adv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	158 <param name="outputs" value="short_summary,missing,image" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	159 </section>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	160 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	161 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	162 <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	163 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	164 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	165 <test expect_num_outputs="4">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	166 <param name="input" value="transcriptome.fa" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	167 <param name="lineage_dataset" value="arthropoda_odb10" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	168 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	169 <param name="mode" value="tran" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	170 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	171 <section name="adv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	172 <param name="auto_lineage" value="--auto-lineage" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	173 <param name="outputs" value="short_summary,missing,image" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	174 </section>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	175 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	176 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	177 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	178 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	179 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	180 <test expect_num_outputs="2">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	181 <param name="input" value="genome.fa" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	182 <param name="lineage_dataset" value="arthropoda_odb10" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	183 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	184 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	185 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	186 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	187 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	188 <param name="augustus_mode" value="builtin" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	189 <param name="augustus_species" value="human" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	190 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	191 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	192 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	193 <section name="adv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	194 <param name="outputs" value="short_summary" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	195 </section>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	196 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	197 <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	198 </test>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	199 <test expect_num_outputs="3">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	200 <param name="input" value="genome.fa" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	201 <param name="lineage_dataset" value="arthropoda_odb10" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	202 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	203 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	204 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	205 <param name="use_augustus_selector" value="yes" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	206 <conditional name="aug_prediction">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	207 <param name="augustus_mode" value="history" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	208 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	209 </conditional>
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 <section name="adv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	213 <param name="outputs" value="short_summary,missing" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	214 </section>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	215 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	216 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	217 <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	218 </test>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	219 <test expect_num_outputs="4">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	220 <param name="input" value="genome.fa" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	221 <param name="lineage_dataset" value="arthropoda_odb10" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	222 <conditional name="busco_mode">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	223 <param name="mode" value="geno" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	224 <conditional name="use_augustus">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	225 <param name="use_augustus_selector" value="no" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	226 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	227 </conditional>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	228 <section name="adv">
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	229 <param name="outputs" value="short_summary,missing,image" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	230 </section>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	231 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	232 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	233 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="4" />
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	234 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
2 382a4c19007f planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 1 diff changeset	235 </test>
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	236 </tests>
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	237 <help><![CDATA[
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	238
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	239
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	240 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	241 --------------------------------------------------------------------------------------------------------------
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	242
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	243 Interpreting the results
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	244 ^^^^^^^^^^^^^^^^^^^^^^^^
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	245
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	246 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	247 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	248 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	249
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	250 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	251 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	252 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	253 (biological) or a chimeric assembly of haplotypes (technical).
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	254 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	255 Therefore you should filter them before a BUSCO analysis.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	256 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	257 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	258 is what you will be aiming for.
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	259
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	260 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	261 .
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	262
4 5ecdeca79a0d planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 iuc parents: 3 diff changeset	263 .. _BUSCO: http://busco.ezlab.org/
9 cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	264
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	265 ]]> </help>
cf13a1e03e5b "planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a" iuc parents: 8 diff changeset	266 <expand macro="citations" />
0 5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 iuc parents: diff changeset	267 </tool>

Mercurial > repos > iuc > busco

annotate busco.xml @ 11:0d243f458b53 draft