Mercurial > repos > iuc > busco

annotate busco.xml @ 23:4e70d88adf2f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 68696449a909c43d0e44bc9cfc8f8945e8a9dfce
author iuc
date Fri, 04 Apr 2025 11:18:42 +0000
parents e5c372c91e46
children
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1 <tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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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 <!-- update augustus_species if update the augustus pin -->
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12 <requirement type="package" version="3.5.0">augustus</requirement>
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13 <requirement type="package" version="1.34">tar</requirement>
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14 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
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15 <!-- TODO might be removed in the future: for some reason conda installs an outdated sepp 4.4.0 but the latest dendropy 5.x which are incompatible -->
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16 <requirement type="package" version="4.5.5">sepp</requirement>
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17 </requirements>
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18 <version_command>busco --version</version_command>
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19 <command><![CDATA[
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20 ## tool tests can not run with --offline (otherwise we would need to store a lot of data at IUC)
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21 ## so we create a mock dir in the working dir where the tool can write to
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22 ##
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23 ## a more thorough test can be executed as follows
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24 ## - set the `test` parameters to `""`
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25 ## - download complete reference DB (~200G, final 105G) to tools/busco/test-data/test-db/busco_downloads
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26 ## ```
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27 ## busco --download_path tools/busco/test-data/test-db/busco_downloads/ --download all
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28 ## find tools/busco/test-data/test-db/busco_downloads/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -exec rm -rf {} \;
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29 ## find tools/busco/test-data/test-db/busco_downloads/placement_files -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -delete
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30 ## find tools/busco/test-data/test-db/busco_downloads/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
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31 ## ```
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32 ## - test containerized (note: test-data is mounted ro in containerized tests)
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33 ##
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34 ## alternatively .. a bit weaker
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35 ## - set the `test` parameters to `""` comment --offline
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36 ## - run test NOT containerized (this will download the data needed for the tests)
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37 ## - uncomment --offline and test containerized
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38 #if $test == 'true'
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39 mkdir mock_db_path/ &&
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40 cp -r '$cached_db.fields.path'/* mock_db_path/ &&
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41 #end if
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42
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43 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'augustus':
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44
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45 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
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46 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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47 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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48
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49 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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50 ## Using an augustus model from history, we need to unzip it and let augustus find it
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51 mkdir -p 'augustus_dir/species/' &&
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52 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
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53 #end if
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54 #end if
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55
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56 #if $input.is_of_type("fasta.gz")
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57 gunzip -c '$input' > input.fa &&
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58 #else
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59 ln -s '$input' input.fa &&
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60 #end if
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61
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62 busco
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63 --in 'input.fa'
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64 --mode '${busco_mode.mode}'
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65 --out busco_galaxy
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66 --cpu \${GALAXY_SLOTS:-4}
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67 --evalue ${adv.evalue}
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68 --limit ${adv.limit}
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69 --contig_break ${adv.contig_break}
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70 #if $test == 'true'
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71 --download_path mock_db_path
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72 #else
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73 --offline
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74 --download_path '$cached_db.fields.path'
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75 #end if
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76
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77 #if $lineage.lineage_mode == "auto_detect":
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78 $lineage.auto_lineage
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79 #else if $lineage.lineage_mode == "select_lineage":
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80 --lineage_dataset '${lineage.lineage_dataset}'
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81 #end if
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82
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83 #if $busco_mode.mode == 'geno':
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84 #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
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85 --miniprot
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86 #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
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87 ${busco_mode.use_augustus.long}
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88 --augustus
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89 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
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90 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
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91 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
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92 --augustus_species local
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93 #end if
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94 #else:
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95 --metaeuk
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96 #end if
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97 #end if
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98
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99 #if $outputs and 'image' in $outputs:
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100 && mkdir BUSCO_summaries
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101 && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
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102 && generate_plot.py -wd BUSCO_summaries -rt specific
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103 #end if
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104
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105 #if $outputs and 'gff' in $outputs:
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106 && echo "\##gff-version 3" > busco_output.gff
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107 ## gff files can be absent
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108 && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true)
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109 #end if
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110 #if $outputs and 'faa' in $outputs:
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111 && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.faa >> busco_output.faa 2> /dev/null || true)
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112 #end if
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113 #if $outputs and 'fna' in $outputs:
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114 && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.fna >> busco_output.fna 2> /dev/null || true)
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115 #end if
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116 ]]></command>
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117 <inputs>
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118 <param name="test" type="hidden"/>
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119 <param type="data" name="input" format="fasta,fasta.gz" 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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120 <param name="cached_db" label="Cached database with lineage" type="select">
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121 <options from_data_table="busco_database">
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122 <validator message="No BUSCO database is available - please contact your Galaxy admin." type="no_options"/>
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123 </options>
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124 </param>
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125 <conditional name="busco_mode">
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126 <param argument="--mode" type="select" label="Mode">
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127 <option value="geno">Genome assemblies (DNA)</option>
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128 <option value="tran">Transcriptome assemblies (DNA)</option>
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129 <option value="prot">Annotated gene sets (protein)</option>
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130 </param>
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131 <when value="geno">
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132 <conditional name="use_augustus">
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133 <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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134 <option value="augustus">Augustus</option>
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135 <option value="metaeuk">Metaeuk</option>
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136 <option value="miniprot" selected="true">Miniprot</option>
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137 </param>
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138 <when value="metaeuk"/>
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139 <when value="miniprot"/>
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140 <when value="augustus">
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141 <conditional name="aug_prediction">
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142 <param name="augustus_mode" type="select" label="Augustus species model">
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143 <option value="no" selected="true">Use the default species for selected lineage</option>
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144 <option value="builtin">Use another predefined species model</option>
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145 <option value="history">Use a custom species model</option>
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146 </param>
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147 <when value="no"/>
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148 <when value="history">
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149 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
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150 </when>
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151 <when value="builtin">
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152 <param name="augustus_species" type="select" label="Augustus species model" help="If model name is different than species name it is shown in parentheses." >
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153 <expand macro="augustus_species"/>
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154 </param>
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155 </when>
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156 </conditional>
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157 <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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158 </when>
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159 </conditional>
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160 </when>
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161 <when value="tran"/>
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162 <when value="prot"/>
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163 </conditional>
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164 <conditional name="lineage">
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165 <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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166 <option value="auto_detect">Auto-detect</option>
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167 <option value="select_lineage">Select lineage</option>
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168 </param>
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169 <when value="auto_detect">
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170 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
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171 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
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172 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
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173 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
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174 </param>
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175 </when>
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176 <when value="select_lineage">
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177 <param argument="--lineage_dataset" type="select" label="Lineage">
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178 <options from_data_table="busco_database_options">
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179 <filter type="param_value" column="2" ref="cached_db"/>
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180 </options>
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181 </param>
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182 </when>
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183 </conditional>
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184
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185 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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186 <option value="short_summary" selected="true">short summary text</option>
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187 <option value="missing">list with missing IDs</option>
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188 <option value="image">summary image</option>
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189 <option value="gff">gff</option>
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190 <option value="faa">Protein sequences</option>
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191 <option value="fna">Nucleotide sequences</option>
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192 </param>
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193
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194 <section name="adv" title="Advanced Options" expanded="False">
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195 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches."/>
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196 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
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197 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
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198 </section>
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199 </inputs>
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200
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201 <outputs>
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202 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
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203 <filter>outputs and 'short_summary' in outputs</filter>
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204 </data>
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205 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
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206 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
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207 <filter>outputs and 'missing' in outputs</filter>
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208 </data>
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209 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
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210 <filter>outputs and 'image' in outputs</filter>
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211 </data>
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212 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
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213 <filter>outputs and 'gff' in outputs</filter>
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214 </data>
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215 <data name='busco_faa' format='fasta' label="${tool.name} on ${on_string}: Protein sequences" from_work_dir="busco_output.faa">
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216 <filter>outputs and 'faa' in outputs</filter>
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217 </data>
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218 <data name='busco_fna' format='fasta' label="${tool.name} on ${on_string}: Nucleotide sequences" from_work_dir="busco_output.fna">
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219 <filter>outputs and 'fna' in outputs</filter>
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220 </data>
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221 </outputs>
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222
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223 <tests>
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224 <!-- <test expect_num_outputs="6">
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225 <param name="test" value="true"/>
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226 <param name="input" value="genome.fa.gz" ftype="fasta.gz"/>
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227 <conditional name="lineage">
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228 <param name="lineage_mode" value="select_lineage"/>
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229 <param name="lineage_dataset" value="arthropoda_odb10"/>
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230 </conditional>
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231 <conditional name="busco_mode">
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232 <param name="mode" value="geno"/>
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233 <conditional name="use_augustus">
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234 <param name="use_augustus_selector" value="augustus"/>
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235 </conditional>
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236 </conditional>
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237 <param name="outputs" value="short_summary,missing,gff,faa,fna"/>
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238 <output name="busco_sum">
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239 <assert_contents>
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240 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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241 <has_text text="Gene predictor used: augustus"/>
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242 </assert_contents>
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243 </output>
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244 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
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245 <output name="busco_gff">
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246 <assert_contents>
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247 <has_n_lines n="1"/>
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248 <has_text text="##gff-version 3"/>
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249 </assert_contents>
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250 </output>
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251 <output name="busco_fna">
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252 <assert_contents>
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253 <has_text text=">"/>
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254 </assert_contents>
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255 </output>
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256 <output name="busco_faa">
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257 <assert_contents>
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258 <has_text text=">"/>
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259 </assert_contents>
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260 </output>
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261 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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262 <assert_stdout>
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263 <has_text text="BUSCO analysis done"/>
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264 </assert_stdout>
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265 </test>
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266 <test expect_num_outputs="5">
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267 <param name="test" value="true"/>
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268 <param name="input" value="proteome.fa"/>
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269 <conditional name="lineage">
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270 <param name="lineage_mode" value="select_lineage"/>
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271 <param name="lineage_dataset" value="arthropoda_odb10"/>
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272 </conditional>
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273 <conditional name="busco_mode">
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274 <param name="mode" value="prot"/>
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275 </conditional>
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276 <param name="outputs" value="short_summary,missing,image,gff"/>
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277 <output name="busco_sum">
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278 <assert_contents>
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279 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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280 <has_text text="BUSCO was run in mode: proteins"/>
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281 </assert_contents>
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282 </output>
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283 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10"/>
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284 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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285 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size"/>
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286 <output name="busco_gff">
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287 <assert_contents>
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288 <has_n_lines n="1"/>
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289 <has_text text="##gff-version 3"/>
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290 </assert_contents>
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291 </output>
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292 <assert_stdout>
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293 <has_text text="BUSCO analysis done"/>
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294 </assert_stdout>
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295 </test>
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296 <test expect_num_outputs="5">
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297 <param name="test" value="true"/>
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298 <param name="input" value="transcriptome.fa"/>
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299 <conditional name="lineage">
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300 <param name="lineage_mode" value="select_lineage"/>
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301 <param name="lineage_dataset" value="arthropoda_odb10"/>
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302 </conditional>
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303 <conditional name="busco_mode">
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304 <param name="mode" value="tran"/>
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305 </conditional>
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306 <param name="outputs" value="short_summary,missing,image,gff"/>
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307 <output name="busco_sum">
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308 <assert_contents>
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309 <has_text text="BUSCO was run in mode: euk_tran"/>
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310 </assert_contents>
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311 </output>
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312 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6"/>
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313 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6"/>
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314 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size"/>
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315 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff"/>
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316 <assert_stdout>
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317 <has_text text="BUSCO analysis done"/>
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318 </assert_stdout>
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319 </test>
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320 <test expect_num_outputs="3">
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321 <param name="test" value="true"/>
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322 <param name="input" value="genome.fa"/>
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323 <conditional name="lineage">
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324 <param name="lineage_mode" value="select_lineage"/>
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325 <param name="lineage_dataset" value="arthropoda_odb10"/>
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326 </conditional>
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327 <conditional name="busco_mode">
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328 <param name="mode" value="geno"/>
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329 <conditional name="use_augustus">
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330 <param name="use_augustus_selector" value="augustus"/>
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331 <conditional name="aug_prediction">
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332 <param name="augustus_mode" value="builtin"/>
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333 <param name="augustus_species" value="human"/>
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334 </conditional>
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335 </conditional>
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336 </conditional>
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337 <param name="outputs" value="short_summary,gff"/>
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338 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
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339 <assert_contents>
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340 <has_text text="# Gene predictor used: augustus"/>
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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/full_table" compare="diff" lines_diff="10"/>
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344 <output name="busco_gff">
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345 <assert_contents>
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346 <has_n_lines n="1"/>
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347 <has_text text="##gff-version 3"/>
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348 </assert_contents>
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349 </output>
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350 <assert_stdout>
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351 <has_text text="BUSCO analysis done"/>
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352 </assert_stdout>
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353 </test>
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354 <test expect_num_outputs="3">
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355 <param name="test" value="true"/>
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356 <param name="input" value="genome.fa"/>
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357 <conditional name="lineage">
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358 <param name="lineage_mode" value="select_lineage"/>
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359 <param name="lineage_dataset" value="arthropoda_odb10"/>
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360 </conditional>
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361 <conditional name="busco_mode">
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362 <param name="mode" value="geno"/>
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363 <conditional name="use_augustus">
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364 <param name="use_augustus_selector" value="augustus"/>
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365 <conditional name="aug_prediction">
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366 <param name="augustus_mode" value="history"/>
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367 <param name="augustus_model" value="local.tar.gz" ftype="augustus"/>
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368 </conditional>
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369 </conditional>
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370 </conditional>
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371 <param name="outputs" value="short_summary,missing"/>
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372 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
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373 <assert_contents>
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374 <has_text text="# Gene predictor used: augustus"/>
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375 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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376 </assert_contents>
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377 </output>
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378 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
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379 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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380 <assert_stdout>
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381 <has_text text="BUSCO analysis done"/>
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382 </assert_stdout>
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383 </test>
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384 <test expect_num_outputs="5">
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385 <param name="test" value="true"/>
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386 <param name="input" value="genome.fa"/>
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387 <conditional name="lineage">
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388 <param name="lineage_mode" value="select_lineage"/>
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389 <param name="lineage_dataset" value="arthropoda_odb10"/>
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390 </conditional>
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391 <conditional name="busco_mode">
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392 <param name="mode" value="geno"/>
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393 <conditional name="use_augustus">
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394 <param name="use_augustus_selector" value="metaeuk"/>
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395 </conditional>
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396 </conditional>
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397 <param name="outputs" value="short_summary,missing,image,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: metaeuk"/>
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401 </assert_contents>
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402 </output>
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403 <output name="busco_table" file="genome_results_metaeuk/full_table">
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404 <assert_contents>
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405 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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406 <has_text text="9647at6656"/>
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407 </assert_contents>
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408 </output>
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409 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
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410 <assert_contents>
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411 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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412 <has_text text="9647at6656"/>
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413 </assert_contents>
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414 </output>
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415 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
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416 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/>
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417 <assert_stdout>
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418 <has_text text="BUSCO analysis done"/>
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419 </assert_stdout>
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420 </test> -->
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421 <test expect_num_outputs="5">
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422 <param name="test" value="true"/>
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423 <param name="input" value="genome.fa"/>
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424 <conditional name="lineage">
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425 <param name="lineage_mode" value="auto_detect"/>
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426 <param name="auto_lineage" value="--auto-lineage"/>
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427 </conditional>
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428 <conditional name="busco_mode">
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429 <param name="mode" value="geno"/>
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430 <conditional name="use_augustus">
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431 <param name="use_augustus_selector" value="metaeuk"/>
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432 </conditional>
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433 </conditional>
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434 <param name="outputs" value="short_summary,missing,image,gff"/>
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435 <output name="busco_sum">
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436 <assert_contents>
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437 <has_text text="Gene predictor used: metaeuk"/>
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438 </assert_contents>
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439 </output>
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440 <output name="busco_table">
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441 <assert_contents>
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442 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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443 <has_text text="The lineage dataset is: eukaryota_odb10"/>
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444 </assert_contents>
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445 </output>
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446 <output name="busco_missing">
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447 <assert_contents>
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448 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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449 <has_text text="The lineage dataset is: eukaryota_odb10"/>
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450 </assert_contents>
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451 </output>
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452 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
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453 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff"/>
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454 <assert_stdout>
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455 <has_text text="BUSCO analysis done"/>
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456 </assert_stdout>
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457 </test>
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458 <!-- <test expect_num_outputs="3">
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459 <param name="test" value="true"/>
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460 <param name="input" value="genome.fa"/>
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461 <conditional name="lineage">
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462 <param name="lineage_mode" value="select_lineage"/>
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463 <param name="lineage_dataset" value="arthropoda_odb10"/>
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464 </conditional>
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465 <param name="outputs" value="short_summary,gff"/>
21
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466 <output name="busco_sum">
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467 <assert_contents>
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468 <has_text text="# Gene predictor used: miniprot"/>
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469 </assert_contents>
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470 </output>
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471 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/>
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472 <output name="busco_table" file="genome_results_miniprot/full_table">
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473 <assert_contents>
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474 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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475 <has_text text="9647at6656"/>
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476 </assert_contents>
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477 </output>
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478 <assert_stdout>
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479 <has_text text="BUSCO analysis done"/>
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480 </assert_stdout>
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481 </test> -->
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482 </tests>
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483 <help><![CDATA[
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484
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485
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486 BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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487 --------------------------------------------------------------------------------------------------------------
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488
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489 Interpreting the results
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490 ^^^^^^^^^^^^^^^^^^^^^^^^
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491
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492 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
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493 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
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494 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
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495
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496 BUSCO completeness results make sense only in the context of the biology of your organism.
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497 You have to understand whether missing or duplicated genes are of biological or technical origin.
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498 For instance, a high level of duplication may be explained by a recent whole duplication event
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499 (biological) or a chimeric assembly of haplotypes (technical).
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500 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
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501 Therefore you should filter them before a BUSCO analysis.
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502 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
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503 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
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504 is what you will be aiming for.
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505
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506 For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
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507 .
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508
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509 .. _BUSCO: http://busco.ezlab.org/
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510
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511 ]]></help>
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512 <expand macro="citations"/>
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513 </tool>