Mercurial > repos > iuc > busco
annotate busco.xml @ 12:1278204240d8 draft
"planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
author | iuc |
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date | Tue, 02 Nov 2021 09:40:29 +0000 |
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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 <xrefs> |
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4 <xref type="bio.tools">busco</xref> |
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5 </xrefs> |
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6 <macros> |
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7 <import>macros.xml</import> |
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8 </macros> |
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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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16 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && |
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17 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && |
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18 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && |
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19 |
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20 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': |
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21 ## Using an augustus model from history, we need to unzip it and let augustus find it |
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22 mkdir -p 'augustus_dir/species/' && |
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23 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' && |
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24 #end if |
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25 |
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26 busco |
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27 --in '${input}' |
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28 --update-data |
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29 --mode '${busco_mode.mode}' |
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30 --out busco_galaxy |
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31 --cpu \${GALAXY_SLOTS:-4} |
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32 --evalue ${adv.evalue} |
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33 --limit ${adv.limit} |
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34 |
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35 #if $lineage.lineage_mode == "auto_detect": |
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36 $lineage.auto_lineage |
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37 #else if $lineage.lineage_mode == "select_lineage": |
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38 --lineage_dataset '${lineage.lineage_dataset}' |
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39 #end if |
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40 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': |
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41 |
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42 ${busco_mode.use_augustus.long} |
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43 --augustus |
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44 |
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45 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin': |
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46 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}' |
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47 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': |
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48 --augustus_species local |
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49 #end if |
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50 #end if |
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51 |
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52 #if $adv.outputs and 'image' in $adv.outputs: |
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53 && |
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54 mkdir BUSCO_summaries |
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55 && |
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56 ls -l busco_galaxy/run_*/ && |
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57 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ |
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58 && |
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59 generate_plot.py -wd BUSCO_summaries -rt specific |
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60 #end if |
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61 |
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62 ]]> </command> |
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63 <inputs> |
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64 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." /> |
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65 <conditional name="busco_mode"> |
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66 <param argument="--mode" type="select" label="Mode"> |
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67 <option value="geno">Genome assemblies (DNA)</option> |
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68 <option value="tran">Transcriptome assemblies (DNA)</option> |
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69 <option value="prot">annotated gene sets (protein)</option> |
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70 </param> |
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71 <when value="geno"> |
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72 <conditional name="use_augustus"> |
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73 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk"> |
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74 <option value="yes">Yes, use Augustus</option> |
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75 <option value="no" selected="true">Use Metaeuk</option> |
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76 </param> |
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77 <when value="no" /> |
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78 <when value="yes"> |
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79 <conditional name="aug_prediction"> |
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80 <param name="augustus_mode" type="select" label="Augustus species model"> |
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81 <option value="no" selected="true">Use the default species for selected lineage</option> |
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82 <option value="builtin">Use another predefined species model</option> |
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83 <option value="history">Use a custom species model</option> |
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84 </param> |
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85 <when value="no" /> |
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86 <when value="history"> |
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87 <param name="augustus_model" type="data" format="augustus" label="Augustus model" /> |
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88 </when> |
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89 <when value="builtin"> |
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90 <param name="augustus_species" type="select" label="Augustus species model"> |
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91 <expand macro="augustus_species" /> |
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92 </param> |
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93 </when> |
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94 </conditional> |
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95 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" /> |
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96 </when> |
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97 </conditional> |
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98 </when> |
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99 <when value="tran" /> |
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100 <when value="prot" /> |
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101 </conditional> |
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102 |
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103 <conditional name="lineage"> |
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104 <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage"> |
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105 <option value="auto_detect">Auto-detect</option> |
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106 <option value="select_lineage">Select lineage</option> |
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107 </param> |
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108 <when value="auto_detect"> |
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109 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage."> |
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110 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option> |
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111 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option> |
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112 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option> |
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113 </param> |
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114 </when> |
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115 <when value="select_lineage"> |
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116 <param argument="--lineage_dataset" type="select" label="Lineage"> |
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117 <expand macro="lineages" /> |
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118 </param> |
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119 </when> |
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120 </conditional> |
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121 |
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122 <section name="adv" title="Advanced Options" expanded="False"> |
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123 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> |
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124 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> |
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125 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> |
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126 <option value="short_summary">short summary text</option> |
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127 <option value="missing">list with missing IDs</option> |
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128 <option value="image">summary image</option> |
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129 </param> |
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130 </section> |
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131 </inputs> |
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132 <outputs> |
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133 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> |
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134 <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter> |
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135 </data> |
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136 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" /> |
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137 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"> |
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138 <filter>adv['outputs'] and 'missing' in adv['outputs']</filter> |
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139 </data> |
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140 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png"> |
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141 <filter>adv['outputs'] and 'image' in adv['outputs']</filter> |
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142 </data> |
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143 </outputs> |
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144 <tests> |
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145 <test expect_num_outputs="3"> |
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146 <param name="input" value="genome.fa" /> |
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147 <conditional name="lineage"> |
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148 <param name="lineage_mode" value="select_lineage" /> |
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149 <param name="lineage_dataset" value="arthropoda_odb10" /> |
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150 </conditional> |
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151 <conditional name="busco_mode"> |
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152 <param name="mode" value="geno" /> |
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153 <conditional name="use_augustus"> |
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154 <param name="use_augustus_selector" value="yes" /> |
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155 </conditional> |
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156 </conditional> |
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157 <section name="adv"> |
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158 <param name="outputs" value="short_summary,missing" /> |
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159 </section> |
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160 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> |
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161 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> |
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162 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"> |
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163 <assert_contents> |
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164 <has_text text="# BUSCO version is: @TOOL_VERSION@" /> |
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165 </assert_contents> |
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166 </output> |
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167 </test> |
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168 <test expect_num_outputs="4"> |
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169 <param name="input" value="proteome.fa" /> |
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170 <conditional name="lineage"> |
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171 <param name="lineage_mode" value="select_lineage" /> |
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172 <param name="lineage_dataset" value="arthropoda_odb10" /> |
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173 </conditional> |
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174 <conditional name="busco_mode"> |
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175 <param name="mode" value="prot" /> |
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176 </conditional> |
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177 <section name="adv"> |
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178 <param name="outputs" value="short_summary,missing,image" /> |
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179 </section> |
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180 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" /> |
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181 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> |
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182 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> |
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183 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> |
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184 </test> |
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185 <test expect_num_outputs="4"> |
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186 <param name="input" value="transcriptome.fa" /> |
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187 <conditional name="lineage"> |
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188 <param name="lineage_mode" value="select_lineage" /> |
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189 <param name="lineage_dataset" value="arthropoda_odb10" /> |
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190 </conditional> |
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191 <conditional name="busco_mode"> |
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192 <param name="mode" value="tran" /> |
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193 </conditional> |
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194 <section name="adv"> |
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195 <param name="outputs" value="short_summary,missing,image" /> |
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196 </section> |
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197 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" /> |
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198 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> |
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199 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> |
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200 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> |
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201 </test> |
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202 <test expect_num_outputs="2"> |
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203 <param name="input" value="genome.fa" /> |
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204 <conditional name="lineage"> |
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205 <param name="lineage_mode" value="select_lineage" /> |
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206 <param name="lineage_dataset" value="arthropoda_odb10" /> |
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207 </conditional> |
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208 <conditional name="busco_mode"> |
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209 <param name="mode" value="geno" /> |
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210 <conditional name="use_augustus"> |
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211 <param name="use_augustus_selector" value="yes" /> |
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212 <conditional name="aug_prediction"> |
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213 <param name="augustus_mode" value="builtin" /> |
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214 <param name="augustus_species" value="human" /> |
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215 </conditional> |
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216 </conditional> |
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217 </conditional> |
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218 <section name="adv"> |
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219 <param name="outputs" value="short_summary" /> |
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220 </section> |
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221 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> |
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222 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> |
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223 </test> |
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224 <test expect_num_outputs="3"> |
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225 <param name="input" value="genome.fa" /> |
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226 <conditional name="lineage"> |
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227 <param name="lineage_mode" value="select_lineage" /> |
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228 <param name="lineage_dataset" value="arthropoda_odb10" /> |
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229 </conditional> |
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230 <conditional name="busco_mode"> |
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231 <param name="mode" value="geno" /> |
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232 <conditional name="use_augustus"> |
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233 <param name="use_augustus_selector" value="yes" /> |
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234 <conditional name="aug_prediction"> |
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235 <param name="augustus_mode" value="history" /> |
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236 <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> |
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237 </conditional> |
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238 </conditional> |
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239 </conditional> |
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240 <section name="adv"> |
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241 <param name="outputs" value="short_summary,missing" /> |
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242 </section> |
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243 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> |
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244 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> |
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245 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> |
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246 </test> |
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247 <test expect_num_outputs="4"> |
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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="no" /> |
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257 </conditional> |
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258 </conditional> |
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259 <section name="adv"> |
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260 <param name="outputs" value="short_summary,missing,image" /> |
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261 </section> |
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262 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" /> |
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263 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> |
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264 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> |
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265 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> |
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266 </test> |
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267 <test expect_num_outputs="4"> |
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268 <param name="input" value="genome.fa" /> |
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269 <conditional name="lineage"> |
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270 <param name="lineage_mode" value="auto_detect" /> |
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271 <param name="auto_lineage" value="--auto-lineage" /> |
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272 </conditional> |
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273 <conditional name="busco_mode"> |
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274 <param name="mode" value="geno" /> |
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275 <conditional name="use_augustus"> |
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276 <param name="use_augustus_selector" value="no" /> |
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277 </conditional> |
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278 </conditional> |
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279 <section name="adv"> |
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280 <param name="outputs" value="short_summary,missing,image" /> |
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281 </section> |
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282 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="4" /> |
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283 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="0" /> |
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284 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="0" /> |
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285 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> |
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286 </test> |
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287 </tests> |
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288 <help><![CDATA[ |
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289 |
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290 |
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291 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs |
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292 -------------------------------------------------------------------------------------------------------------- |
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293 |
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294 Interpreting the results |
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295 ^^^^^^^^^^^^^^^^^^^^^^^^ |
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296 |
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297 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a |
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298 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete |
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299 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs. |
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300 |
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301 BUSCO completeness results make sense only in the context of the biology of your organism. |
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302 You have to understand whether missing or duplicated genes are of biological or technical origin. |
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303 For instance, a high level of duplication may be explained by a recent whole duplication event |
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304 (biological) or a chimeric assembly of haplotypes (technical). |
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305 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates. |
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306 Therefore you should filter them before a BUSCO analysis. |
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307 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment |
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308 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples |
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309 is what you will be aiming for. |
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310 |
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311 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_ |
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312 . |
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313 |
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314 .. _BUSCO: http://busco.ezlab.org/ |
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315 |
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316 ]]> </help> |
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317 <expand macro="citations" /> |
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318 </tool> |