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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
author iuc
date Sat, 04 Oct 2025 17:47:40 +0000
parents c209d02621e7
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!-- TODO might be removed in the future: for some reason conda installs an outdated sepp 4.4.0 but the latest dendropy 5.x which are incompatible --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/busco_downloads/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -exec rm -rf {} \;
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29 ## find tools/busco/test-data/busco_downloads/placement_files -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -delete
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30 ## find tools/busco/test-data/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
8
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96 #end if
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97 #end if
19
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98
22
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99 #if $lineage.lineage_mode != "auto_detect":
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100 && cp busco_galaxy/run_*/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv
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101 && cp busco_galaxy/run_*/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv
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102 #if $outputs and 'image' in $outputs:
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103 && mkdir BUSCO_summaries
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104 && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
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105 && generate_plot.py -wd BUSCO_summaries -rt specific
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106 && cp BUSCO_summaries/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png
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107 #end if
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108
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109 #if $outputs and 'gff' in $outputs:
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110 && echo "\##gff-version 3" > busco_galaxy/busco_output.gff
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111 ## gff files can be absent
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112 && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)
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113 #end if
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114 #if $outputs and 'faa' in $outputs:
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115 && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_specific.faa 2> /dev/null || true)
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116 #end if
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117 #if $outputs and 'fna' in $outputs:
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118 && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_specific.fna 2> /dev/null || true)
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119 #end if
3
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120 #end if
0
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121
22
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122 ## if $lineage.lineage_mode == "auto_detect", BUSCO output several files with the same name, causing an issue, we need to rename the files
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123 #if $lineage.lineage_mode == "auto_detect":
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124 && specific_lineage=\$(find ./busco_galaxy -name "short_summary.specific.*.txt" | head -n 1 | cut -d'.' -f4)
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125 && generic_lineage=\$(find ./busco_galaxy -name "short_summary.generic.*.txt" | head -n 1 | cut -d'.' -f4)
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126
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127 ##Rename the output files to differenciate specific and generic lineages results
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128 ## Full table
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129 && cp busco_galaxy/run_\${specific_lineage}/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv
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130 && cp busco_galaxy/run_\${generic_lineage}/full_table.tsv busco_galaxy/full_table_generic_lineage.tsv
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131 ##Missing busco list
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132 && cp busco_galaxy/run_\${specific_lineage}/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv
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133 && cp busco_galaxy/run_\${generic_lineage}/missing_busco_list.tsv busco_galaxy/missing_busco_list_generic_lineage.tsv
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134 #if $outputs and 'image' in $outputs:
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135 && mkdir BUSCO_summaries_specific
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136 && cp busco_galaxy/short_summary.specific.*.txt BUSCO_summaries_specific/
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137 && generate_plot.py -wd BUSCO_summaries_specific -rt specific
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138 && cp BUSCO_summaries_specific/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png
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139 && mkdir BUSCO_summaries_generic
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140 && cp busco_galaxy/short_summary.generic.*.txt BUSCO_summaries_generic/
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141 && generate_plot.py -wd BUSCO_summaries_generic -rt generic
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142 && cp BUSCO_summaries_generic/busco_figure.png busco_galaxy/busco_figure_generic_lineage.png
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143 #end if
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144 #if $outputs and 'gff' in $outputs:
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145 ## gff files can be absent
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146 && echo "\##gff-version 3" > busco_galaxy/busco_output_specific.gff
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147 && (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)
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148 && echo "\##gff-version 3" > busco_galaxy/busco_output_generic.gff
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149 && (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_generic.gff 2> /dev/null || true)
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150 #end if
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151 #if $outputs and 'faa' in $outputs:
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152 && (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_specific.faa 2> /dev/null || true)
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153 && (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_generic.faa 2> /dev/null || true)
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154 #end if
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155 #if $outputs and 'fna' in $outputs:
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156 && (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_specific.fna 2> /dev/null || true)
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157 && (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_generic.fna 2> /dev/null || true)
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158 #end if
21
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159 #end if
20
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160 ]]></command>
0
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161 <inputs>
21
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162 <param name="test" type="hidden"/>
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163 <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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164 <param name="cached_db" label="Cached database with lineage" type="select">
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165 <options from_data_table="busco_database">
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166 <validator message="No BUSCO database is available - please contact your Galaxy admin." type="no_options"/>
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167 </options>
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168 </param>
8
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169 <conditional name="busco_mode">
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170 <param argument="--mode" type="select" label="Mode">
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171 <option value="geno">Genome assemblies (DNA)</option>
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172 <option value="tran">Transcriptome assemblies (DNA)</option>
21
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173 <option value="prot">Annotated gene sets (protein)</option>
8
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174 </param>
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175 <when value="geno">
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176 <conditional name="use_augustus">
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177 <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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178 <option value="augustus">Augustus</option>
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179 <option value="metaeuk">Metaeuk</option>
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180 <option value="miniprot" selected="true">Miniprot</option>
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181 </param>
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182 <when value="metaeuk"/>
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183 <when value="miniprot"/>
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184 <when value="augustus">
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185 <conditional name="aug_prediction">
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186 <param name="augustus_mode" type="select" label="Augustus species model">
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187 <option value="no" selected="true">Use the default species for selected lineage</option>
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188 <option value="builtin">Use another predefined species model</option>
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189 <option value="history">Use a custom species model</option>
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190 </param>
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191 <when value="no"/>
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192 <when value="history">
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193 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
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194 </when>
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195 <when value="builtin">
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196 <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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197 <expand macro="augustus_species"/>
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198 </param>
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199 </when>
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200 </conditional>
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201 <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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202 </when>
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203 </conditional>
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204 </when>
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205 <when value="tran"/>
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206 <when value="prot"/>
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207 </conditional>
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208 <conditional name="lineage">
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209 <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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210 <option value="auto_detect">Auto-detect</option>
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211 <option value="select_lineage">Select lineage</option>
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212 </param>
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213 <when value="auto_detect">
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214 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
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215 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
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216 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
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217 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
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218 </param>
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219 <param name="generic_results" type="boolean" checked="false" label="Do you want to display the results from the generic lineage" help="BUSCO generates files for the parent lineage (generic) and the final selected lineage (specific). Generally, the lineage to select for your assessments should be the most specific lineage available. The generic lineage datasets for the domains archaea, bacteria and eukaryota."/>
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220 </when>
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221 <when value="select_lineage">
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222 <param argument="--lineage_dataset" type="select" label="Lineage">
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223 <options from_data_table="busco_database_options">
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224 <filter type="param_value" column="2" ref="cached_db"/>
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225 </options>
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226 </param>
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227 </when>
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228 </conditional>
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229
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230 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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231 <option value="short_summary" selected="true">Short summary text</option>
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232 <option value="missing">List with missing IDs</option>
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233 <option value="image">Summary image</option>
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234 <option value="gff">gff</option>
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235 <option value="faa">Protein sequences</option>
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236 <option value="fna">Nucleotide sequences</option>
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237 </param>
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238
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239 <section name="adv" title="Advanced Options" expanded="False">
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240 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches."/>
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241 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
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242 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
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243 </section>
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244 </inputs>
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245
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246 <outputs>
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247 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: Short summary - Specific lineage" from_work_dir="busco_galaxy/short_summary.specific.*.txt">
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248 <filter>outputs and 'short_summary' in outputs</filter>
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249 </data>
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250 <data name='busco_sum_generic' format='txt' label="${tool.name} on ${on_string}: Short summary - Generic lineage" from_work_dir="busco_galaxy/short_summary.generic.*.txt">
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251 <filter>(outputs and 'short_summary' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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252 </data>
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253 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: Full table - Specific lineage" from_work_dir="busco_galaxy/full_table_specific_lineage.tsv">
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254 </data>
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255 <data name='busco_table_generic' format='tabular' label="${tool.name} on ${on_string}: Full table - Generic lineage" from_work_dir="busco_galaxy/full_table_generic_lineage.tsv">
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256 <filter>lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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257 </data>
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258 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: Missing buscos - Specific lineage" from_work_dir="busco_galaxy/missing_busco_list_specific_lineage.tsv">
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259 <filter>outputs and 'missing' in outputs</filter>
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260 </data>
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261 <data name='busco_missing_generic' format='tabular' label="${tool.name} on ${on_string}: Missing buscos - Generic lineage" from_work_dir="busco_galaxy/missing_busco_list_generic_lineage.tsv">
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262 <filter>(outputs and 'missing' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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263 </data>
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264 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: Summary image - Specific lineage" from_work_dir="busco_galaxy/busco_figure_specific_lineage.png">
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265 <filter>outputs and 'image' in outputs</filter>
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266 </data>
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267 <data name='summary_image_generic' format='png' label="${tool.name} on ${on_string}: Summary image - Generic lineage" from_work_dir="busco_galaxy/busco_figure_generic_lineage.png">
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268 <filter>(outputs and 'image' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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269 </data>
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270 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF - Specific lineage" from_work_dir="busco_galaxy/busco_output_specific.gff">
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271 <filter>outputs and 'gff' in outputs</filter>
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272 </data>
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273 <data name='busco_gff_generic' format='gff3' label="${tool.name} on ${on_string}: GFF - Generic lineage" from_work_dir="busco_galaxy/busco_output_generic.gff">
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274 <filter>(outputs and 'gff' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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275 </data>
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276 <data name='busco_faa' format='fasta' label="${tool.name} on ${on_string}: Protein sequences - Specific lineage" from_work_dir="busco_galaxy/busco_output_specific.faa">
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277 <filter>outputs and 'faa' in outputs</filter>
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278 </data>
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279 <data name='busco_faa_generic' format='fasta' label="${tool.name} on ${on_string}: Protein sequences - Generic lineage" from_work_dir="busco_galaxy/busco_output_generic.faa">
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280 <filter>(outputs and 'faa' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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281 </data>
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282 <data name='busco_fna' format='fasta' label="${tool.name} on ${on_string}: Nucleotide sequences - Specific lineage" from_work_dir="busco_galaxy/busco_output_specific.fna">
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283 <filter>outputs and 'fna' in outputs</filter>
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284 </data>
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285 <data name='busco_fna_generic' format='fasta' label="${tool.name} on ${on_string}: Nucleotide sequences - Generic lineage" from_work_dir="busco_galaxy/busco_output_generic.fna">
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286 <filter>(outputs and 'fna' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
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287 </data>
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288 </outputs>
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289
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290
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291 <tests>
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292 <!-- <test expect_num_outputs="6">
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293 <param name="test" value="true"/>
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294 <param name="input" value="genome.fa.gz" ftype="fasta.gz"/>
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295 <conditional name="lineage">
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296 <param name="lineage_mode" value="select_lineage"/>
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297 <param name="lineage_dataset" value="arthropoda_odb10"/>
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298 </conditional>
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299 <conditional name="busco_mode">
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300 <param name="mode" value="geno"/>
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301 <conditional name="use_augustus">
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302 <param name="use_augustus_selector" value="augustus"/>
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303 </conditional>
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304 </conditional>
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305 <param name="outputs" value="short_summary,missing,gff,faa,fna"/>
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306 <output name="busco_sum">
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307 <assert_contents>
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308 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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309 <has_text text="Gene predictor used: augustus"/>
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310 </assert_contents>
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311 </output>
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312 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
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313 <output name="busco_gff">
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314 <assert_contents>
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315 <has_n_lines n="1"/>
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316 <has_text text="##gff-version 3"/>
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317 </assert_contents>
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318 </output>
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319 <output name="busco_fna">
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320 <assert_contents>
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321 <has_text text=">"/>
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322 </assert_contents>
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323 </output>
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324 <output name="busco_faa">
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325 <assert_contents>
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326 <has_text text=">"/>
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327 </assert_contents>
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328 </output>
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329 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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330 <assert_stdout>
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331 <has_text text="BUSCO analysis done"/>
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332 </assert_stdout>
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333 </test>
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334 <test expect_num_outputs="5">
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335 <param name="test" value="true"/>
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336 <param name="input" value="proteome.fa"/>
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337 <conditional name="lineage">
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338 <param name="lineage_mode" value="select_lineage"/>
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339 <param name="lineage_dataset" value="arthropoda_odb10"/>
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340 </conditional>
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341 <conditional name="busco_mode">
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342 <param name="mode" value="prot"/>
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343 </conditional>
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344 <param name="outputs" value="short_summary,missing,image,gff"/>
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345 <output name="busco_sum">
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346 <assert_contents>
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347 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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348 <has_text text="BUSCO was run in mode: proteins"/>
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349 </assert_contents>
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350 </output>
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351 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10"/>
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352 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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353 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size"/>
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354 <output name="busco_gff">
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355 <assert_contents>
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356 <has_n_lines n="1"/>
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357 <has_text text="##gff-version 3"/>
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358 </assert_contents>
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359 </output>
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360 <assert_stdout>
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361 <has_text text="BUSCO analysis done"/>
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362 </assert_stdout>
0
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363 </test>
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364 <test expect_num_outputs="5">
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365 <param name="test" value="true"/>
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366 <param name="input" value="transcriptome.fa"/>
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367 <conditional name="lineage">
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368 <param name="lineage_mode" value="select_lineage"/>
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369 <param name="lineage_dataset" value="arthropoda_odb10"/>
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370 </conditional>
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371 <conditional name="busco_mode">
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372 <param name="mode" value="tran"/>
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373 </conditional>
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374 <param name="outputs" value="short_summary,missing,image,gff"/>
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375 <output name="busco_sum">
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376 <assert_contents>
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377 <has_text text="BUSCO was run in mode: euk_tran"/>
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378 </assert_contents>
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379 </output>
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380 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6"/>
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381 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6"/>
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382 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size"/>
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383 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff"/>
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384 <assert_stdout>
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385 <has_text text="BUSCO analysis done"/>
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386 </assert_stdout>
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387 </test>
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388 <test expect_num_outputs="3">
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389 <param name="test" value="true"/>
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390 <param name="input" value="genome.fa"/>
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391 <conditional name="lineage">
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392 <param name="lineage_mode" value="select_lineage"/>
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393 <param name="lineage_dataset" value="arthropoda_odb10"/>
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394 </conditional>
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395 <conditional name="busco_mode">
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396 <param name="mode" value="geno"/>
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397 <conditional name="use_augustus">
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398 <param name="use_augustus_selector" value="augustus"/>
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399 <conditional name="aug_prediction">
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400 <param name="augustus_mode" value="builtin"/>
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401 <param name="augustus_species" value="human"/>
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402 </conditional>
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403 </conditional>
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404 </conditional>
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405 <param name="outputs" value="short_summary,gff"/>
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406 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
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407 <assert_contents>
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408 <has_text text="# Gene predictor used: augustus"/>
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409 </assert_contents>
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410 </output>
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411 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
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412 <output name="busco_gff">
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413 <assert_contents>
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414 <has_n_lines n="1"/>
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415 <has_text text="##gff-version 3"/>
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416 </assert_contents>
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417 </output>
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418 <assert_stdout>
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419 <has_text text="BUSCO analysis done"/>
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420 </assert_stdout>
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421 </test>
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422 <test expect_num_outputs="3">
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423 <param name="test" value="true"/>
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424 <param name="input" value="genome.fa"/>
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425 <conditional name="lineage">
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426 <param name="lineage_mode" value="select_lineage"/>
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427 <param name="lineage_dataset" value="arthropoda_odb10"/>
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428 </conditional>
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429 <conditional name="busco_mode">
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430 <param name="mode" value="geno"/>
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431 <conditional name="use_augustus">
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432 <param name="use_augustus_selector" value="augustus"/>
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433 <conditional name="aug_prediction">
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434 <param name="augustus_mode" value="history"/>
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435 <param name="augustus_model" value="local.tar.gz" ftype="augustus"/>
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436 </conditional>
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437 </conditional>
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438 </conditional>
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439 <param name="outputs" value="short_summary,missing"/>
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440 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
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441 <assert_contents>
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442 <has_text text="# Gene predictor used: augustus"/>
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443 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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444 </assert_contents>
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445 </output>
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446 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
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447 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
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448 <assert_stdout>
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449 <has_text text="BUSCO analysis done"/>
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450 </assert_stdout>
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451 </test>
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452 <test expect_num_outputs="5">
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453 <param name="test" value="true"/>
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454 <param name="input" value="genome.fa"/>
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455 <conditional name="lineage">
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456 <param name="lineage_mode" value="select_lineage"/>
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457 <param name="lineage_dataset" value="arthropoda_odb10"/>
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458 </conditional>
8
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459 <conditional name="busco_mode">
20
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460 <param name="mode" value="geno"/>
8
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461 <conditional name="use_augustus">
20
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462 <param name="use_augustus_selector" value="metaeuk"/>
8
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463 </conditional>
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464 </conditional>
20
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465 <param name="outputs" value="short_summary,missing,image,gff"/>
19
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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: metaeuk"/>
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469 </assert_contents>
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470 </output>
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471 <output name="busco_table" file="genome_results_metaeuk/full_table">
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472 <assert_contents>
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473 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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474 <has_text text="9647at6656"/>
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475 </assert_contents>
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476 </output>
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477 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
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478 <assert_contents>
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479 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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480 <has_text text="9647at6656"/>
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481 </assert_contents>
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482 </output>
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483 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
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484 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/>
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485 <assert_stdout>
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486 <has_text text="BUSCO analysis done"/>
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487 </assert_stdout>
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488 </test> -->
22
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489 <test expect_num_outputs="2">
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490 <param name="test" value="true"/>
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491 <param name="input" value="bacilli_odb_test.fasta"/>
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492 <conditional name="lineage">
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diff changeset
493 <param name="lineage_mode" value="auto_detect"/>
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494 <param name="auto_lineage" value="--auto-lineage-prok"/>
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495 </conditional>
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496 <conditional name="busco_mode">
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497 <param name="mode" value="geno"/>
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498 </conditional>
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499 <param name="outputs" value="short_summary"/>
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500 <output name="busco_sum">
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501 <assert_contents>
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502 <has_text text="Gene predictor used: prodigal"/>
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diff changeset
503 </assert_contents>
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504 </output>
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505 <output name="busco_table">
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506 <assert_contents>
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507 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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diff changeset
508 <has_text text="The lineage dataset is: bacilli_odb10"/>
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509 </assert_contents>
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diff changeset
510 </output>
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511 </test>
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diff changeset
512 <test expect_num_outputs="10">
21
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diff changeset
513 <param name="test" value="true"/>
20
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diff changeset
514 <param name="input" value="genome.fa"/>
12
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parents: 11
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515 <conditional name="lineage">
20
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diff changeset
516 <param name="lineage_mode" value="auto_detect"/>
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diff changeset
517 <param name="auto_lineage" value="--auto-lineage"/>
22
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diff changeset
518 <param name="generic_results" value="true"/>
12
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parents: 11
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519 </conditional>
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diff changeset
520 <conditional name="busco_mode">
20
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521 <param name="mode" value="geno"/>
12
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522 <conditional name="use_augustus">
20
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parents: 19
diff changeset
523 <param name="use_augustus_selector" value="metaeuk"/>
12
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524 </conditional>
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525 </conditional>
20
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diff changeset
526 <param name="outputs" value="short_summary,missing,image,gff"/>
19
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527 <output name="busco_sum">
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528 <assert_contents>
22
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diff changeset
529 <has_text text="Gene predictor used: prodigal"/>
5dd4f18b0d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
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parents: 21
diff changeset
530 </assert_contents>
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diff changeset
531 </output>
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iuc
parents: 21
diff changeset
532 <output name="busco_sum_generic">
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parents: 21
diff changeset
533 <assert_contents>
5dd4f18b0d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
iuc
parents: 21
diff changeset
534 <has_text text="Gene predictor used: prodigal"/>
19
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parents: 18
diff changeset
535 </assert_contents>
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536 </output>
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parents: 18
diff changeset
537 <output name="busco_table">
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538 <assert_contents>
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539 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
22
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parents: 21
diff changeset
540 <has_text text="The lineage dataset is: "/>
5dd4f18b0d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
iuc
parents: 21
diff changeset
541 </assert_contents>
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diff changeset
542 </output>
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iuc
parents: 21
diff changeset
543 <output name="busco_table_generic">
5dd4f18b0d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
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parents: 21
diff changeset
544 <assert_contents>
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iuc
parents: 21
diff changeset
545 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
5dd4f18b0d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
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diff changeset
546 <has_text text="The lineage dataset is: "/>
19
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parents: 18
diff changeset
547 </assert_contents>
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iuc
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diff changeset
548 </output>
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549 <output name="busco_missing">
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550 <assert_contents>
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551 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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552 <has_text text="The lineage dataset is: "/>
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553 </assert_contents>
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554 </output>
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555 <output name="busco_missing_generic">
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556 <assert_contents>
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557 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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558 <has_text text="The lineage dataset is: "/>
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559 </assert_contents>
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560 </output>
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561 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
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562 <output name="summary_image_generic" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
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563 <output name="busco_gff">
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564 <assert_contents>
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565 <has_text text="##gff-version 3"/>
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566 </assert_contents>
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567 </output>
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568 <output name="busco_gff_generic">
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569 <assert_contents>
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570 <has_text text="##gff-version 3"/>
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571 </assert_contents>
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572 </output>
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573 <assert_stdout>
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574 <has_text text="BUSCO analysis done"/>
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575 </assert_stdout>
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576 </test>
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577 <!-- <test expect_num_outputs="3">
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578 <param name="test" value="true"/>
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579 <param name="input" value="genome.fa"/>
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580 <conditional name="lineage">
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581 <param name="lineage_mode" value="select_lineage"/>
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582 <param name="lineage_dataset" value="arthropoda_odb10"/>
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583 </conditional>
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584 <param name="outputs" value="short_summary,gff"/>
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585 <output name="busco_sum">
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586 <assert_contents>
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587 <has_text text="# Gene predictor used: miniprot"/>
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588 </assert_contents>
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589 </output>
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590 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/>
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591 <output name="busco_table" file="genome_results_miniprot/full_table">
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592 <assert_contents>
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593 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
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594 <has_text text="9647at6656"/>
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595 </assert_contents>
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596 </output>
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597 <assert_stdout>
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598 <has_text text="BUSCO analysis done"/>
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599 </assert_stdout>
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600 </test> -->
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601 </tests>
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602 <help><![CDATA[
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603
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604
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605 BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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606 --------------------------------------------------------------------------------------------------------------
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607
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608 Interpreting the results
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609 ^^^^^^^^^^^^^^^^^^^^^^^^
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610
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611 BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
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612 genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
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613 and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
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614
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615 BUSCO completeness results make sense only in the context of the biology of your organism.
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616 You have to understand whether missing or duplicated genes are of biological or technical origin.
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617 For instance, a high level of duplication may be explained by a recent whole duplication event
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618 (biological) or a chimeric assembly of haplotypes (technical).
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619 Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
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620 Therefore you should filter them before a BUSCO analysis.
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621 Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
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622 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
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623 is what you will be aiming for.
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624
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625 For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
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626 .
0
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627
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628 .. _BUSCO: http://busco.ezlab.org/
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629
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630 ]]></help>
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631 <expand macro="citations"/>
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632 </tool>