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annotate busco.xml @ 19:2a5b8b9936bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
author iuc
date Tue, 14 Nov 2023 13:03:37 +0000
parents 94170eee0ad8
children ea8146ee148f
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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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28
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29 #end if
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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 --contig_break ${adv.contig_break}
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39
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40 #if $lineage_conditional.selector == 'cached':
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41 --offline
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42 --download_path $lineage_conditional.cached_db.fields.path
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43 #else
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44 --update-data
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45 #end if
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46
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47 #if $lineage.lineage_mode == "auto_detect":
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48 $lineage.auto_lineage
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49 #else if $lineage.lineage_mode == "select_lineage":
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50 --lineage_dataset '${lineage.lineage_dataset}'
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51 #end if
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52
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53 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
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54
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55 ${busco_mode.use_augustus.long}
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56 --augustus
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57
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58 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
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59 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
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60 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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61 --augustus_species local
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62 #end if
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63 #end if
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65 #if str( $busco_mode.mode ) == "geno":
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66 #if $busco_mode.miniprot:
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67 --miniprot
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68 #end if
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69 #end if
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70
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71 #if $outputs and 'image' in $outputs:
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72 &&
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73 mkdir BUSCO_summaries
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74 &&
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75 ls -l busco_galaxy/run_*/ &&
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76 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
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77 &&
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78 generate_plot.py -wd BUSCO_summaries -rt specific
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79 #end if
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80
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81 #if $outputs and 'gff' in $outputs:
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82 &&
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83 echo "\##gff-version 3" > busco_output.gff
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84 &&
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85 ## gff files can be absent
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86 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
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87 #end if
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88
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89
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90 ]]> </command>
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91 <inputs>
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92 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
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93 <conditional name="lineage_conditional">
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94 <param name="selector" type="select" label="Lineage data source">
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95 <option value="download">Download lineage data</option>
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96 <option value="cached">Use cached lineage data</option>
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97 </param>
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98 <when value="cached">
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99 <param name="cached_db" label="Cached database with lineage" type="select">
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100 <options from_data_table="busco_database">
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101 <validator message="No BUSCO database is available" type="no_options" />
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102 </options>
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103 </param>
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104 </when>
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105 <when value="download"/>
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106 </conditional>
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107 <conditional name="busco_mode">
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108 <param argument="--mode" type="select" label="Mode">
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109 <option value="geno">Genome assemblies (DNA)</option>
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110 <option value="tran">Transcriptome assemblies (DNA)</option>
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111 <option value="prot">annotated gene sets (protein)</option>
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112 </param>
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113 <when value="geno">
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114 <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>
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115 <conditional name="use_augustus">
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116 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
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117 <option value="yes">Yes, use Augustus</option>
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118 <option value="no" selected="true">Use Metaeuk</option>
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119 </param>
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120 <when value="no" />
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121 <when value="yes">
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122 <conditional name="aug_prediction">
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123 <param name="augustus_mode" type="select" label="Augustus species model">
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124 <option value="no" selected="true">Use the default species for selected lineage</option>
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125 <option value="builtin">Use another predefined species model</option>
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126 <option value="history">Use a custom species model</option>
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127 </param>
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128 <when value="no" />
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129 <when value="history">
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130 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
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131 </when>
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132 <when value="builtin">
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133 <param name="augustus_species" type="select" label="Augustus species model">
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134 <expand macro="augustus_species" />
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135 </param>
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136 </when>
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137 </conditional>
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138 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" />
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139 </when>
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140 </conditional>
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141 </when>
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142 <when value="tran" />
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143 <when value="prot" />
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144 </conditional>
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145
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146 <conditional name="lineage">
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147 <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage">
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148 <option value="auto_detect">Auto-detect</option>
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149 <option value="select_lineage">Select lineage</option>
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150 </param>
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151 <when value="auto_detect">
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152 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
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153 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
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154 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
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155 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
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156 </param>
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157 </when>
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158 <when value="select_lineage">
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159 <param argument="--lineage_dataset" type="select" label="Lineage">
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160 <expand macro="lineages" />
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161 </param>
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162 </when>
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163 </conditional>
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164
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165 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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166 <option value="short_summary" selected="true">short summary text</option>
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167 <option value="missing">list with missing IDs</option>
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168 <option value="image">summary image</option>
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169 <option value="gff">gff</option>
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170 </param>
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171
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172 <section name="adv" title="Advanced Options" expanded="False">
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173 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
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174 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
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175 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
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176 </section>
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177 </inputs>
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178
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179 <outputs>
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180 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
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181 <filter>outputs and 'short_summary' in outputs</filter>
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182 </data>
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183 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
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184 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
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185 <filter>outputs and 'missing' in outputs</filter>
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186 </data>
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187 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
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188 <filter>outputs and 'image' in outputs</filter>
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189 </data>
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190 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
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191 <filter>outputs and 'gff' in outputs</filter>
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192 </data>
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193 <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
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194 <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
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195 </data>
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196 </outputs>
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197
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198 <tests>
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199 <test expect_num_outputs="4">
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200 <param name="input" value="genome.fa" />
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201 <conditional name="lineage">
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202 <param name="lineage_mode" value="select_lineage" />
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203 <param name="lineage_dataset" value="arthropoda_odb10" />
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204 </conditional>
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205 <conditional name="busco_mode">
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206 <param name="mode" value="geno" />
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207 <conditional name="use_augustus">
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208 <param name="use_augustus_selector" value="yes" />
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209 </conditional>
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210 </conditional>
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211 <param name="outputs" value="short_summary,missing,gff" />
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212 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
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213 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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214 <output name="busco_gff">
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215 <assert_contents>
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216 <has_n_lines n="1"/>
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217 <has_text text="##gff-version 3" />
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218 </assert_contents>
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219 </output>
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220 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
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221 <assert_contents>
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222 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
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223 </assert_contents>
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224 </output>
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225 </test>
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226 <test expect_num_outputs="5">
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227 <param name="input" value="proteome.fa" />
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228 <conditional name="lineage">
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229 <param name="lineage_mode" value="select_lineage" />
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230 <param name="lineage_dataset" value="arthropoda_odb10" />
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231 </conditional>
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232 <conditional name="busco_mode">
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233 <param name="mode" value="prot" />
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234 </conditional>
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235 <param name="outputs" value="short_summary,missing,image,gff" />
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236 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" />
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237 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
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238 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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239 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
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240 <output name="busco_gff">
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241 <assert_contents>
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242 <has_n_lines n="1"/>
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243 <has_text text="##gff-version 3" />
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244 </assert_contents>
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245 </output>
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246 </test>
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247 <test expect_num_outputs="5">
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248 <param name="input" value="transcriptome.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="tran" />
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255 </conditional>
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256 <param name="outputs" value="short_summary,missing,image,gff" />
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257 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
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258 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
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259 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
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260 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
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261 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
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262 </test>
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263 <test expect_num_outputs="4">
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264 <param name="input" value="genome.fa" />
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265 <conditional name="lineage">
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266 <param name="lineage_mode" value="select_lineage" />
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267 <param name="lineage_dataset" value="arthropoda_odb10" />
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268 </conditional>
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269 <conditional name="busco_mode">
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270 <param name="mode" value="geno" />
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271 <param name="miniprot" value="true"/>
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272 <conditional name="use_augustus">
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273 <param name="use_augustus_selector" value="yes" />
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274 <conditional name="aug_prediction">
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275 <param name="augustus_mode" value="builtin" />
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276 <param name="augustus_species" value="human" />
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277 </conditional>
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278 </conditional>
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279 </conditional>
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280 <param name="outputs" value="short_summary,gff" />
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281 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
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282 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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283 <output name="busco_gff">
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284 <assert_contents>
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285 <has_n_lines n="1"/>
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286 <has_text text="##gff-version 3" />
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287 </assert_contents>
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288 </output>
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289 <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
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290 <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
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291 </test>
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292 <test expect_num_outputs="3">
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293 <param name="input" value="genome.fa" />
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294 <conditional name="lineage">
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295 <param name="lineage_mode" value="select_lineage" />
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296 <param name="lineage_dataset" value="arthropoda_odb10" />
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297 </conditional>
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298 <conditional name="busco_mode">
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299 <param name="mode" value="geno" />
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300 <conditional name="use_augustus">
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301 <param name="use_augustus_selector" value="yes" />
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302 <conditional name="aug_prediction">
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303 <param name="augustus_mode" value="history" />
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304 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
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305 </conditional>
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306 </conditional>
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307 </conditional>
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308 <param name="outputs" value="short_summary,missing" />
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309 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
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310 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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311 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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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="select_lineage" />
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317 <param name="lineage_dataset" value="arthropoda_odb10" />
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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/short_summary" compare="diff" lines_diff="6" />
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327 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
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328 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
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329 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
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330 <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
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331 </test>
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332 <test expect_num_outputs="5">
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333 <param name="input" value="genome.fa" />
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334 <conditional name="lineage">
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335 <param name="lineage_mode" value="auto_detect" />
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336 <param name="auto_lineage" value="--auto-lineage" />
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337 </conditional>
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338 <conditional name="busco_mode">
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339 <param name="mode" value="geno" />
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340 <conditional name="use_augustus">
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341 <param name="use_augustus_selector" value="no" />
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342 </conditional>
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343 </conditional>
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344 <param name="outputs" value="short_summary,missing,image,gff" />
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345 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
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346 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
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347 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
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348 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
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349 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
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350 </test>
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351 <test expect_num_outputs="2">
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352 <param name="input" value="genome.fa" />
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353 <conditional name="lineage_conditional">
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354 <param name="selector" value="cached"/>
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355 <param name="cached_db" value="busco-demo-db-20230328"/>
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356 </conditional>
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357 <conditional name="lineage">
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358 <param name="lineage_mode" value="select_lineage" />
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359 <param name="lineage_dataset" value="archaea_odb10" />
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360 </conditional>
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361 <param name="outputs" value="short_summary" />
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362 <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" />
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363 <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" />
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364 <assert_stdout>
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365 <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/>
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366 </assert_stdout>
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367 </test>
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368 </tests>
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369 <help><![CDATA[
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370
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371
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372 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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373 --------------------------------------------------------------------------------------------------------------
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374
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375 Interpreting the results
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376 ^^^^^^^^^^^^^^^^^^^^^^^^
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377
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378 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
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379 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
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380 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
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381
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382 BUSCO completeness results make sense only in the context of the biology of your organism.
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383 You have to understand whether missing or duplicated genes are of biological or technical origin.
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384 For instance, a high level of duplication may be explained by a recent whole duplication event
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385 (biological) or a chimeric assembly of haplotypes (technical).
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386 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
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387 Therefore you should filter them before a BUSCO analysis.
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388 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
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389 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
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390 is what you will be aiming for.
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391
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392 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
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393 .
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394
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395 .. _BUSCO: http://busco.ezlab.org/
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396
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397 ]]> </help>
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398 <expand macro="citations" />
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399 </tool>