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annotate busco.xml @ 18:0e63a4c4c908 draft

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planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
author iuc
date Fri, 14 Apr 2023 08:13:19 +0000
parents eba1f3c7cd64
children 1b5840963240
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1 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>assess genome assembly and annotation completeness</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">busco</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
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11 <requirement type="package" version="1.34">tar</requirement>
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12 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
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13 </requirements>
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14 <version_command>busco --version</version_command>
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15 <command><![CDATA[
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17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
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19 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
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20 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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21 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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23 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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24 ## Using an augustus model from history, we need to unzip it and let augustus find it
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25 mkdir -p 'augustus_dir/species/' &&
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26 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
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27 #end if
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29 #end if
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30
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31 busco
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32 --in '${input}'
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33 --mode '${busco_mode.mode}'
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34 --out busco_galaxy
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35 --cpu \${GALAXY_SLOTS:-4}
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36 --evalue ${adv.evalue}
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37 --limit ${adv.limit}
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38
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39 #if $lineage_conditional.selector == 'cached':
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40 --offline
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41 --download_path $lineage_conditional.cached_db.fields.path
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42 #else
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43 --update-data
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44 #end if
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45
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46 #if $lineage.lineage_mode == "auto_detect":
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47 $lineage.auto_lineage
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48 #else if $lineage.lineage_mode == "select_lineage":
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49 --lineage_dataset '${lineage.lineage_dataset}'
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50 #end if
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51 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
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52
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53 ${busco_mode.use_augustus.long}
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54 --augustus
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55
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56 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
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57 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
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58 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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59 --augustus_species local
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60 #end if
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61 #end if
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62
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63 #if $outputs and 'image' in $outputs:
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64 &&
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65 mkdir BUSCO_summaries
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66 &&
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67 ls -l busco_galaxy/run_*/ &&
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68 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
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69 &&
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70 generate_plot.py -wd BUSCO_summaries -rt specific
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71 #end if
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72
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73 #if $outputs and 'gff' in $outputs:
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74 &&
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75 echo "\##gff-version 3" > busco_output.gff
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76 &&
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77 ## gff files can be absent
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78 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
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79 #end if
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80
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81 ]]> </command>
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82 <inputs>
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83 <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." />
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84 <conditional name="lineage_conditional">
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85 <param name="selector" type="select" label="Lineage data source">
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86 <option value="download">Download lineage data</option>
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87 <option value="cached">Use cached lineage data</option>
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88 </param>
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89 <when value="cached">
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90 <param name="cached_db" label="Cached database with lineage" type="select">
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91 <options from_data_table="busco_database">
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92 <validator message="No BUSCO database is available" type="no_options" />
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93 </options>
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94 </param>
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95 </when>
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96 <when value="download"/>
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97 </conditional>
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98 <conditional name="busco_mode">
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99 <param argument="--mode" type="select" label="Mode">
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100 <option value="geno">Genome assemblies (DNA)</option>
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101 <option value="tran">Transcriptome assemblies (DNA)</option>
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102 <option value="prot">annotated gene sets (protein)</option>
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103 </param>
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104 <when value="geno">
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105 <conditional name="use_augustus">
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106 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
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107 <option value="yes">Yes, use Augustus</option>
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108 <option value="no" selected="true">Use Metaeuk</option>
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109 </param>
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110 <when value="no" />
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111 <when value="yes">
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112 <conditional name="aug_prediction">
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113 <param name="augustus_mode" type="select" label="Augustus species model">
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114 <option value="no" selected="true">Use the default species for selected lineage</option>
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115 <option value="builtin">Use another predefined species model</option>
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116 <option value="history">Use a custom species model</option>
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117 </param>
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118 <when value="no" />
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119 <when value="history">
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120 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
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121 </when>
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122 <when value="builtin">
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123 <param name="augustus_species" type="select" label="Augustus species model">
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124 <expand macro="augustus_species" />
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125 </param>
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126 </when>
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127 </conditional>
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128 <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" />
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129 </when>
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130 </conditional>
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131 </when>
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132 <when value="tran" />
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133 <when value="prot" />
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134 </conditional>
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135
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136 <conditional name="lineage">
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137 <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">
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138 <option value="auto_detect">Auto-detect</option>
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139 <option value="select_lineage">Select lineage</option>
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140 </param>
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141 <when value="auto_detect">
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142 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
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143 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
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144 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
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145 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
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146 </param>
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147 </when>
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148 <when value="select_lineage">
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149 <param argument="--lineage_dataset" type="select" label="Lineage">
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150 <expand macro="lineages" />
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151 </param>
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152 </when>
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153 </conditional>
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154
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155 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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156 <option value="short_summary" selected="true">short summary text</option>
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157 <option value="missing">list with missing IDs</option>
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158 <option value="image">summary image</option>
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159 <option value="gff">gff</option>
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160 </param>
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161
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162 <section name="adv" title="Advanced Options" expanded="False">
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163 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
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164 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
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165 </section>
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166 </inputs>
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167 <outputs>
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168 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
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169 <filter>outputs and 'short_summary' in outputs</filter>
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170 </data>
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171 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
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172 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
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173 <filter>outputs and 'missing' in outputs</filter>
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174 </data>
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175 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
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176 <filter>outputs and 'image' in outputs</filter>
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177 </data>
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178 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
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179 <filter>outputs and 'gff' in outputs</filter>
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180 </data>
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181 </outputs>
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182 <tests>
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183 <test expect_num_outputs="4">
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184 <param name="input" value="genome.fa" />
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185 <conditional name="lineage">
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186 <param name="lineage_mode" value="select_lineage" />
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187 <param name="lineage_dataset" value="arthropoda_odb10" />
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188 </conditional>
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189 <conditional name="busco_mode">
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190 <param name="mode" value="geno" />
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191 <conditional name="use_augustus">
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192 <param name="use_augustus_selector" value="yes" />
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193 </conditional>
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194 </conditional>
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195 <param name="outputs" value="short_summary,missing,gff" />
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196 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
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197 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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198 <output name="busco_gff">
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199 <assert_contents>
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200 <has_n_lines n="1"/>
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201 <has_text text="##gff-version 3" />
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202 </assert_contents>
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203 </output>
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204 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
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205 <assert_contents>
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206 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
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207 </assert_contents>
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208 </output>
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209 </test>
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210 <test expect_num_outputs="5">
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211 <param name="input" value="proteome.fa" />
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212 <conditional name="lineage">
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213 <param name="lineage_mode" value="select_lineage" />
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214 <param name="lineage_dataset" value="arthropoda_odb10" />
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215 </conditional>
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216 <conditional name="busco_mode">
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217 <param name="mode" value="prot" />
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218 </conditional>
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219 <param name="outputs" value="short_summary,missing,image,gff" />
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220 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" />
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221 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
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222 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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223 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
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224 <output name="busco_gff">
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225 <assert_contents>
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226 <has_n_lines n="1"/>
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227 <has_text text="##gff-version 3" />
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228 </assert_contents>
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229 </output>
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230 </test>
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231 <test expect_num_outputs="5">
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232 <param name="input" value="transcriptome.fa" />
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233 <conditional name="lineage">
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234 <param name="lineage_mode" value="select_lineage" />
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235 <param name="lineage_dataset" value="arthropoda_odb10" />
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236 </conditional>
8
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237 <conditional name="busco_mode">
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238 <param name="mode" value="tran" />
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239 </conditional>
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240 <param name="outputs" value="short_summary,missing,image,gff" />
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241 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
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242 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
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243 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
8
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244 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
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245 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
0
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246 </test>
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247 <test expect_num_outputs="3">
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248 <param name="input" value="genome.fa" />
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249 <conditional name="lineage">
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250 <param name="lineage_mode" value="select_lineage" />
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251 <param name="lineage_dataset" value="arthropoda_odb10" />
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252 </conditional>
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253 <conditional name="busco_mode">
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254 <param name="mode" value="geno" />
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255 <conditional name="use_augustus">
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256 <param name="use_augustus_selector" value="yes" />
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257 <conditional name="aug_prediction">
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258 <param name="augustus_mode" value="builtin" />
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259 <param name="augustus_species" value="human" />
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260 </conditional>
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261 </conditional>
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262 </conditional>
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263 <param name="outputs" value="short_summary,gff" />
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264 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
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265 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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266 <output name="busco_gff">
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267 <assert_contents>
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268 <has_n_lines n="1"/>
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269 <has_text text="##gff-version 3" />
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270 </assert_contents>
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271 </output>
2
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272 </test>
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273 <test expect_num_outputs="3">
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274 <param name="input" value="genome.fa" />
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275 <conditional name="lineage">
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276 <param name="lineage_mode" value="select_lineage" />
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277 <param name="lineage_dataset" value="arthropoda_odb10" />
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278 </conditional>
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279 <conditional name="busco_mode">
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280 <param name="mode" value="geno" />
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281 <conditional name="use_augustus">
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282 <param name="use_augustus_selector" value="yes" />
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283 <conditional name="aug_prediction">
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284 <param name="augustus_mode" value="history" />
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285 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
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286 </conditional>
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287 </conditional>
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288 </conditional>
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289 <param name="outputs" value="short_summary,missing" />
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290 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
8
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291 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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292 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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293 </test>
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294 <test expect_num_outputs="5">
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295 <param name="input" value="genome.fa" />
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296 <conditional name="lineage">
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297 <param name="lineage_mode" value="select_lineage" />
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298 <param name="lineage_dataset" value="arthropoda_odb10" />
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299 </conditional>
8
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300 <conditional name="busco_mode">
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301 <param name="mode" value="geno" />
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302 <conditional name="use_augustus">
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303 <param name="use_augustus_selector" value="no" />
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304 </conditional>
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305 </conditional>
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306 <param name="outputs" value="short_summary,missing,image,gff" />
12
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307 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
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308 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
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309 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
8
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310 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
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311 <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
2
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312 </test>
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313 <test expect_num_outputs="5">
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314 <param name="input" value="genome.fa" />
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315 <conditional name="lineage">
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316 <param name="lineage_mode" value="auto_detect" />
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317 <param name="auto_lineage" value="--auto-lineage" />
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318 </conditional>
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319 <conditional name="busco_mode">
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320 <param name="mode" value="geno" />
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321 <conditional name="use_augustus">
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322 <param name="use_augustus_selector" value="no" />
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323 </conditional>
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324 </conditional>
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325 <param name="outputs" value="short_summary,missing,image,gff" />
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326 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
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327 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
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328 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
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329 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
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330 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
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331 </test>
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332 <test expect_num_outputs="2">
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333 <param name="input" value="genome.fa" />
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334 <conditional name="lineage_conditional">
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335 <param name="selector" value="cached"/>
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336 <param name="cached_db" value="busco-demo-db-20230328"/>
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337 </conditional>
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338 <conditional name="lineage">
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339 <param name="lineage_mode" value="select_lineage" />
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340 <param name="lineage_dataset" value="archaea_odb10" />
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341 </conditional>
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342 <param name="outputs" value="short_summary" />
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343 <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" />
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344 <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" />
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345 <assert_stdout>
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346 <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/>
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347 </assert_stdout>
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348 </test>
0
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349 </tests>
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350 <help><![CDATA[
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351
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352
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353 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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354 --------------------------------------------------------------------------------------------------------------
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355
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356 Interpreting the results
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357 ^^^^^^^^^^^^^^^^^^^^^^^^
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358
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359 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
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360 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
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361 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
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362
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363 BUSCO completeness results make sense only in the context of the biology of your organism.
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364 You have to understand whether missing or duplicated genes are of biological or technical origin.
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365 For instance, a high level of duplication may be explained by a recent whole duplication event
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366 (biological) or a chimeric assembly of haplotypes (technical).
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367 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
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368 Therefore you should filter them before a BUSCO analysis.
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369 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
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370 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
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371 is what you will be aiming for.
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372
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373 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
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374 .
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375
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376 .. _BUSCO: http://busco.ezlab.org/
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377
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378 ]]> </help>
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379 <expand macro="citations" />
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380 </tool>