annotate busco.xml @ 9:cf13a1e03e5b draft

"planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"
author iuc
date Mon, 15 Mar 2021 21:27:17 +0000
parents 602fb8e63aa7
children 0d243f458b53
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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 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
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8 <requirement type="package" version="1.32">tar</requirement>
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9 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
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10 </requirements>
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11 <version_command>busco --version</version_command>
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12 <command><![CDATA[
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13 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
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14 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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15 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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16
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17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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18 ## Using an augustus model from history, we need to unzip it and let augustus find it
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19 mkdir -p 'augustus_dir/species/' &&
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20 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
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21 #end if
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22
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23 busco
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24 --in '${input}'
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25 --lineage_dataset '${lineage_dataset}'
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26 --update-data
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27 --mode '${busco_mode.mode}'
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28 --out busco_galaxy
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29 --cpu \${GALAXY_SLOTS:-4}
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30 --evalue ${adv.evalue}
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31 --limit ${adv.limit}
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32
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33 #if $adv.auto_lineage:
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34 $adv.auto_lineage
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35 #end if
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36 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
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38 ${busco_mode.use_augustus.long}
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39 --augustus
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41 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
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42 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
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43 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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44 --augustus_species local
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45 #end if
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46 #end if
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47
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48 #if $adv.outputs and 'image' in $adv.outputs:
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49 &&
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50 mkdir BUSCO_summaries
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51 &&
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52 ls -l busco_galaxy/run_*/ &&
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53 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
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54 &&
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55 generate_plot.py -wd BUSCO_summaries -rt specific
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56 #end if
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57
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58 ]]> </command>
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59 <inputs>
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60 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
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61 <conditional name="busco_mode">
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62 <param argument="--mode" type="select" label="Mode">
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63 <option value="geno">Genome assemblies (DNA)</option>
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64 <option value="tran">Transcriptome assemblies (DNA)</option>
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65 <option value="prot">annotated gene sets (protein)</option>
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66 </param>
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67 <when value="geno">
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68 <conditional name="use_augustus">
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69 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
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70 <option value="yes">Yes, use Augustus</option>
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71 <option value="no" selected="true">Use Metaeuk</option>
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72 </param>
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73 <when value="no" />
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74 <when value="yes">
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75 <conditional name="aug_prediction">
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76 <param name="augustus_mode" type="select" label="Augustus species model">
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77 <option value="no" selected="true">Use the default species for selected lineage</option>
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78 <option value="builtin">Use another predefined species model</option>
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79 <option value="history">Use a custom species model</option>
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80 </param>
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81 <when value="no" />
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82 <when value="history">
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83 <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
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84 </when>
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85 <when value="builtin">
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86 <param name="augustus_species" type="select" label="Augustus species model">
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87 <expand macro="augustus_species" />
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88 </param>
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89 </when>
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90 </conditional>
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91 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" />
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92 </when>
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93 </conditional>
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94 </when>
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95 <when value="tran" />
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96 <when value="prot" />
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97 </conditional>
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98
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99 <param argument="--lineage_dataset" type="select" label="Lineage">
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100 <expand macro="lineages" />
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101 </param>
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102
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103 <section name="adv" title="Advanced Options" expanded="False">
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104 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
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105 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
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106 <param name="auto_lineage" type="select" optional="true" label="Run auto-lineage to find optimal lineage path">
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107 <option value="--auto-lineage">Run auto-lineage to find optimum lineage path</option>
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108 <option value="--auto-lineage-prok">Run auto-lineage just on non-eukaryote trees to find optimum lineage path</option>
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109 <option value="--auto-lineage-euk">Run auto-placement just on eukaryote tree to find optimum lineage path</option>
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110 </param>
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111 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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112 <option value="short_summary">short summary text</option>
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113 <option value="missing">list with missing IDs</option>
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114 <option value="image">summary image</option>
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115 </param>
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116 </section>
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117 </inputs>
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118 <outputs>
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119 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
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120 <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter>
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121 </data>
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122 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
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123 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
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124 <filter>adv['outputs'] and 'missing' in adv['outputs']</filter>
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125 </data>
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126 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
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127 <filter>adv['outputs'] and 'image' in adv['outputs']</filter>
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128 </data>
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129 </outputs>
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130 <tests>
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131 <test expect_num_outputs="3">
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132 <param name="input" value="genome.fa" />
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133 <param name="lineage_dataset" value="arthropoda_odb10" />
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134 <conditional name="busco_mode">
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135 <param name="mode" value="geno" />
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136 <conditional name="use_augustus">
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137 <param name="use_augustus_selector" value="yes" />
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138 </conditional>
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139 </conditional>
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140 <section name="adv">
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141 <param name="outputs" value="short_summary,missing" />
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142 </section>
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143 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
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144 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
8
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145 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
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146 <assert_contents>
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147 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
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148 </assert_contents>
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149 </output>
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150 </test>
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151 <test expect_num_outputs="4">
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152 <param name="input" value="proteome.fa" />
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153 <param name="lineage_dataset" value="arthropoda_odb10" />
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154 <conditional name="busco_mode">
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155 <param name="mode" value="prot" />
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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,image" />
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159 </section>
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160 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
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161 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
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162 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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163 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
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164 </test>
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165 <test expect_num_outputs="4">
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166 <param name="input" value="transcriptome.fa" />
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167 <param name="lineage_dataset" value="arthropoda_odb10" />
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168 <conditional name="busco_mode">
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169 <param name="mode" value="tran" />
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170 </conditional>
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171 <section name="adv">
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172 <param name="auto_lineage" value="--auto-lineage" />
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173 <param name="outputs" value="short_summary,missing,image" />
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174 </section>
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175 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4" />
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176 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4" />
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177 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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178 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
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179 </test>
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180 <test expect_num_outputs="2">
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181 <param name="input" value="genome.fa" />
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182 <param name="lineage_dataset" value="arthropoda_odb10" />
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183 <conditional name="busco_mode">
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184 <param name="mode" value="geno" />
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185 <conditional name="use_augustus">
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186 <param name="use_augustus_selector" value="yes" />
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187 <conditional name="aug_prediction">
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188 <param name="augustus_mode" value="builtin" />
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189 <param name="augustus_species" value="human" />
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190 </conditional>
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191 </conditional>
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192 </conditional>
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193 <section name="adv">
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194 <param name="outputs" value="short_summary" />
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195 </section>
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196 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
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197 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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198 </test>
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199 <test expect_num_outputs="3">
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200 <param name="input" value="genome.fa" />
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201 <param name="lineage_dataset" value="arthropoda_odb10" />
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202 <conditional name="busco_mode">
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203 <param name="mode" value="geno" />
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204 <conditional name="use_augustus">
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205 <param name="use_augustus_selector" value="yes" />
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206 <conditional name="aug_prediction">
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207 <param name="augustus_mode" value="history" />
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208 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
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209 </conditional>
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210 </conditional>
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211 </conditional>
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212 <section name="adv">
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213 <param name="outputs" value="short_summary,missing" />
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214 </section>
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215 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
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216 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
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217 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
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218 </test>
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219 <test expect_num_outputs="4">
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220 <param name="input" value="genome.fa" />
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221 <param name="lineage_dataset" value="arthropoda_odb10" />
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222 <conditional name="busco_mode">
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223 <param name="mode" value="geno" />
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224 <conditional name="use_augustus">
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225 <param name="use_augustus_selector" value="no" />
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226 </conditional>
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227 </conditional>
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228 <section name="adv">
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229 <param name="outputs" value="short_summary,missing,image" />
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230 </section>
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231 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="4" />
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232 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="4" />
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233 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="4" />
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234 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
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235 </test>
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236 </tests>
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237 <help><![CDATA[
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238
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239
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240 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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241 --------------------------------------------------------------------------------------------------------------
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242
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243 Interpreting the results
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244 ^^^^^^^^^^^^^^^^^^^^^^^^
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245
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246 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
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247 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
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248 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
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249
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250 BUSCO completeness results make sense only in the context of the biology of your organism.
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251 You have to understand whether missing or duplicated genes are of biological or technical origin.
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252 For instance, a high level of duplication may be explained by a recent whole duplication event
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253 (biological) or a chimeric assembly of haplotypes (technical).
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254 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
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255 Therefore you should filter them before a BUSCO analysis.
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256 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
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257 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
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258 is what you will be aiming for.
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259
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260 For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
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261 .
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262
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263 .. _BUSCO: http://busco.ezlab.org/
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264
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265 ]]> </help>
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266 <expand macro="citations" />
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267 </tool>