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annotate busco.xml @ 21:2babe6d5c561 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a
author iuc
date Fri, 30 Aug 2024 15:19:56 +0000
parents ea8146ee148f
children e5c372c91e46
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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 == 'augustus':
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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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22
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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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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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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 #end if
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44
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45 #if $lineage.lineage_mode == "auto_detect":
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46 $lineage.auto_lineage
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47 #else if $lineage.lineage_mode == "select_lineage":
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48 --lineage_dataset '${lineage.lineage_dataset}'
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49 #end if
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51 #if $busco_mode.mode == 'geno':
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52 #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
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53 --miniprot
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54 #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
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55 ${busco_mode.use_augustus.long}
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56 --augustus
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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 #else:
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64 --metaeuk
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65 #end if
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66 #end if
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68 #if $outputs and 'image' in $outputs:
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69 &&
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70 mkdir BUSCO_summaries
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71 &&
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72 ls -l busco_galaxy/run_*/ &&
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73 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
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74 &&
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75 generate_plot.py -wd BUSCO_summaries -rt specific
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76 #end if
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77
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78 #if $outputs and 'gff' in $outputs:
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79 &&
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80 echo "\##gff-version 3" > busco_output.gff
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81 &&
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82 ## gff files can be absent
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83 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
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84 #end if
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85
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86
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87 ]]> </command>
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88 <inputs>
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89 <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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90 <conditional name="lineage_conditional">
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91 <param name="selector" type="select" label="Lineage data source">
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92 <option value="download">Download lineage data</option>
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93 <option value="cached">Use cached lineage data</option>
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94 </param>
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95 <when value="cached">
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96 <param name="cached_db" label="Cached database with lineage" type="select">
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97 <options from_data_table="busco_database">
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98 <validator message="No BUSCO database is available" type="no_options" />
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99 </options>
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100 </param>
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101 </when>
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102 <when value="download"/>
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103 </conditional>
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104 <conditional name="busco_mode">
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105 <param argument="--mode" type="select" label="Mode">
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106 <option value="geno">Genome assemblies (DNA)</option>
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107 <option value="tran">Transcriptome assemblies (DNA)</option>
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108 <option value="prot">annotated gene sets (protein)</option>
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109 </param>
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110 <when value="geno">
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111 <conditional name="use_augustus">
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112 <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">
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113 <option value="augustus">Augustus</option>
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114 <option value="metaeuk">Metaeuk</option>
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115 <option value="miniprot" selected="true">Miniprot</option>
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116
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117 </param>
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118 <when value="metaeuk"/>
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119 <when value="miniprot"/>
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120 <when value="augustus">
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121 <conditional name="aug_prediction">
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122 <param name="augustus_mode" type="select" label="Augustus species model">
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123 <option value="no" selected="true">Use the default species for selected lineage</option>
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124 <option value="builtin">Use another predefined species model</option>
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125 <option value="history">Use a custom species model</option>
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126 </param>
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127 <when value="no" />
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128 <when value="history">
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129 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
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130 </when>
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131 <when value="builtin">
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132 <param name="augustus_species" type="select" label="Augustus species model">
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133 <expand macro="augustus_species" />
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134 </param>
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135 </when>
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136 </conditional>
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137 <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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138 </when>
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139 </conditional>
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140 </when>
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141 <when value="tran" />
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142 <when value="prot" />
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143 </conditional>
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144
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145 <conditional name="lineage">
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146 <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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147 <option value="auto_detect">Auto-detect</option>
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148 <option value="select_lineage">Select lineage</option>
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149 </param>
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150 <when value="auto_detect">
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151 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
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152 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
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153 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
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154 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
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155 </param>
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156 </when>
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157 <when value="select_lineage">
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158 <param argument="--lineage_dataset" type="select" label="Lineage">
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159 <expand macro="lineages" />
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160 </param>
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161 </when>
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162 </conditional>
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163
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164 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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165 <option value="short_summary" selected="true">short summary text</option>
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166 <option value="missing">list with missing IDs</option>
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167 <option value="image">summary image</option>
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168 <option value="gff">gff</option>
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169 </param>
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170
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171 <section name="adv" title="Advanced Options" expanded="False">
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172 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
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173 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
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174 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
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175 </section>
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176 </inputs>
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177
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178 <outputs>
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179 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
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180 <filter>outputs and 'short_summary' in outputs</filter>
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181 </data>
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182 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
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183 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
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184 <filter>outputs and 'missing' in outputs</filter>
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185 </data>
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186 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
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187 <filter>outputs and 'image' in outputs</filter>
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188 </data>
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189 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
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190 <filter>outputs and 'gff' in outputs</filter>
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191 </data>
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192 </outputs>
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193
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194 <tests>
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195 <test expect_num_outputs="4">
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196 <param name="input" value="genome.fa" />
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197 <conditional name="lineage">
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198 <param name="lineage_mode" value="select_lineage" />
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199 <param name="lineage_dataset" value="arthropoda_odb10" />
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200 </conditional>
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201 <conditional name="busco_mode">
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202 <param name="mode" value="geno" />
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203 <conditional name="use_augustus">
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204 <param name="use_augustus_selector" value="augustus" />
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205 </conditional>
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206 </conditional>
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207 <param name="outputs" value="short_summary,missing,gff" />
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208 <output name="busco_sum">
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209 <assert_contents>
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210 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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211 <has_text text="Gene predictor used: augustus"/>
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212 </assert_contents>
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213 </output>
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214 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
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215 <output name="busco_gff">
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216 <assert_contents>
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217 <has_n_lines n="1"/>
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218 <has_text text="##gff-version 3" />
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219 </assert_contents>
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220 </output>
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221 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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222 </test>
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223 <test expect_num_outputs="5">
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224 <param name="input" value="proteome.fa" />
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225 <conditional name="lineage">
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226 <param name="lineage_mode" value="select_lineage" />
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227 <param name="lineage_dataset" value="arthropoda_odb10" />
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228 </conditional>
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229 <conditional name="busco_mode">
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230 <param name="mode" value="prot" />
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231 </conditional>
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232 <param name="outputs" value="short_summary,missing,image,gff" />
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233 <output name="busco_sum">
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234 <assert_contents>
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235 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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236 <has_text text="BUSCO was run in mode: proteins" />
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237 </assert_contents>
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238 </output>
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239 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" />
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240 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" />
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241 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
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242 <output name="busco_gff">
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243 <assert_contents>
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244 <has_n_lines n="1"/>
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245 <has_text text="##gff-version 3" />
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246 </assert_contents>
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247 </output>
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248 </test>
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249 <test expect_num_outputs="5">
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250 <param name="input" value="transcriptome.fa" />
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251 <conditional name="lineage">
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252 <param name="lineage_mode" value="select_lineage" />
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253 <param name="lineage_dataset" value="arthropoda_odb10" />
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254 </conditional>
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255 <conditional name="busco_mode">
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256 <param name="mode" value="tran" />
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257 </conditional>
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258 <param name="outputs" value="short_summary,missing,image,gff" />
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259 <output name="busco_sum">
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260 <assert_contents>
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261 <has_text text="BUSCO was run in mode: euk_tran" />
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262 </assert_contents>
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263 </output>
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264 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
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265 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
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266 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
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267 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
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268 </test>
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269 <test expect_num_outputs="3">
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270 <param name="input" value="genome.fa" />
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271 <conditional name="lineage">
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272 <param name="lineage_mode" value="select_lineage" />
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273 <param name="lineage_dataset" value="arthropoda_odb10" />
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274 </conditional>
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275 <conditional name="busco_mode">
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276 <param name="mode" value="geno" />
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277 <conditional name="use_augustus">
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278 <param name="use_augustus_selector" value="augustus" />
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279 <conditional name="aug_prediction">
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280 <param name="augustus_mode" value="builtin" />
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281 <param name="augustus_species" value="human" />
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282 </conditional>
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283 </conditional>
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284 </conditional>
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285 <param name="outputs" value="short_summary,gff" />
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286 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
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287 <assert_contents>
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288 <has_text text="# Gene predictor used: augustus"/>
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289 </assert_contents>
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290 </output>
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291 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
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292 <output name="busco_gff">
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293 <assert_contents>
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294 <has_n_lines n="1"/>
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295 <has_text text="##gff-version 3" />
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296 </assert_contents>
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297 </output>
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298 </test>
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299 <test expect_num_outputs="3">
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300 <param name="input" value="genome.fa" />
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301 <conditional name="lineage">
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302 <param name="lineage_mode" value="select_lineage" />
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303 <param name="lineage_dataset" value="arthropoda_odb10" />
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304 </conditional>
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305 <conditional name="busco_mode">
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306 <param name="mode" value="geno" />
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307 <conditional name="use_augustus">
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308 <param name="use_augustus_selector" value="augustus" />
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309 <conditional name="aug_prediction">
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310 <param name="augustus_mode" value="history" />
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311 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
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312 </conditional>
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313 </conditional>
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314 </conditional>
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315 <param name="outputs" value="short_summary,missing" />
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316 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
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317 <assert_contents>
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318 <has_text text="# Gene predictor used: augustus"/>
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319 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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320 </assert_contents>
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321 </output>
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322 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
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323 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" />
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324 </test>
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325 <test expect_num_outputs="5">
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326 <param name="input" value="genome.fa" />
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327 <conditional name="lineage">
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328 <param name="lineage_mode" value="select_lineage" />
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329 <param name="lineage_dataset" value="arthropoda_odb10" />
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330 </conditional>
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331 <conditional name="busco_mode">
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332 <param name="mode" value="geno" />
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333 <conditional name="use_augustus">
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334 <param name="use_augustus_selector" value="metaeuk" />
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335 </conditional>
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336 </conditional>
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337 <param name="outputs" value="short_summary,missing,image,gff" />
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338 <output name="busco_sum">
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339 <assert_contents>
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340 <has_text text="# Gene predictor used: metaeuk"/>
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341 </assert_contents>
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342 </output>
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343 <output name="busco_table" file="genome_results_metaeuk/full_table">
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344 <assert_contents>
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345 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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346 <has_text text="9647at6656"/>
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347 </assert_contents>
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348 </output>
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349 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
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350 <assert_contents>
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351 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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352 <has_text text="9647at6656"/>
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353 </assert_contents>
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354 </output>
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355 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
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356 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" />
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357 </test>
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358 <test expect_num_outputs="5">
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359 <param name="input" value="genome.fa" />
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360 <conditional name="lineage">
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361 <param name="lineage_mode" value="auto_detect" />
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362 <param name="auto_lineage" value="--auto-lineage" />
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363 </conditional>
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364 <conditional name="busco_mode">
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365 <param name="mode" value="geno" />
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366 <conditional name="use_augustus">
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367 <param name="use_augustus_selector" value="metaeuk" />
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368 </conditional>
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369 </conditional>
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370 <param name="outputs" value="short_summary,missing,image,gff" />
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371 <output name="busco_sum">
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372 <assert_contents>
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373 <has_text text="Gene predictor used: metaeuk"/>
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374 </assert_contents>
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375 </output>
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376 <output name="busco_table">
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377 <assert_contents>
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378 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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379 <has_text text="The lineage dataset is: eukaryota_odb10"/>
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380 </assert_contents>
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381 </output>
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382 <output name="busco_missing">
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383 <assert_contents>
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384 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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385 <has_text text="The lineage dataset is: eukaryota_odb10"/>
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386 </assert_contents>
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387 </output>
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388 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
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389 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
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390 </test>
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391 <test expect_num_outputs="3">
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392 <param name="input" value="genome.fa" />
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393 <conditional name="lineage">
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394 <param name="lineage_mode" value="select_lineage" />
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395 <param name="lineage_dataset" value="arthropoda_odb10" />
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396 </conditional>
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397 <param name="outputs" value="short_summary,gff" />
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398 <output name="busco_sum">
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399 <assert_contents>
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400 <has_text text="# Gene predictor used: miniprot"/>
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401 </assert_contents>
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402 </output>
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403 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />
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404 <output name="busco_table" file="genome_results_miniprot/full_table">
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405 <assert_contents>
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406 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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407 <has_text text="9647at6656"/>
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408 </assert_contents>
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409 </output>
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410 </test>
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411 </tests>
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412 <help><![CDATA[
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413
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414
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415 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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416 --------------------------------------------------------------------------------------------------------------
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417
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418 Interpreting the results
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419 ^^^^^^^^^^^^^^^^^^^^^^^^
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420
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421 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
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422 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
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423 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
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424
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425 BUSCO completeness results make sense only in the context of the biology of your organism.
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426 You have to understand whether missing or duplicated genes are of biological or technical origin.
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427 For instance, a high level of duplication may be explained by a recent whole duplication event
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428 (biological) or a chimeric assembly of haplotypes (technical).
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429 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
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430 Therefore you should filter them before a BUSCO analysis.
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431 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
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432 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
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433 is what you will be aiming for.
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434
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435 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
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436 .
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437
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438 .. _BUSCO: http://busco.ezlab.org/
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439
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440 ]]> </help>
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441 <expand macro="citations" />
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442 </tool>