Mercurial > repos > iuc > busco

annotate busco.xml @ 7:4048d82f0c88 draft

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"planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c"
author iuc
date Mon, 17 Aug 2020 06:50:18 -0400
parents 1e62c28ba91d
children 602fb8e63aa7
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1 <tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@">
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2 <description>assess genome assembly and annotation completeness</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
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8 <requirement type="package" version="1.32">tar</requirement>
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9 </requirements>
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10 <command><![CDATA[
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11 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
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12 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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13 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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14
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15 #if $adv.aug_prediction.augustus_mode == 'history':
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16 ## Using an augustus model from history, we need to unzip it and let augustus find it
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17 mkdir -p 'augustus_dir/species/' &&
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18 tar -C 'augustus_dir/species/' -xzf '${adv.aug_prediction.augustus_model}' &&
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19 #end if
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20
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21 busco
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22 --in '${input}'
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23 --lineage_dataset '${lineage_dataset}'
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24 --update-data
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25 --mode '${mode}'
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26 -o busco_galaxy
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27 --cpu \${GALAXY_SLOTS:-4}
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28 --evalue ${adv.evalue}
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29 ${adv.long}
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30 --limit ${adv.limit}
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31 #if $adv.aug_prediction.augustus_mode == 'builtin':
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32 --augustus_species '${adv.aug_prediction.augustus_species}'
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33 #else if $adv.aug_prediction.augustus_mode == 'history':
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34 --augustus_species local
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35 #end if
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36 ]]></command>
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37
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38 <inputs>
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39 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
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40 <param argument="--mode" type="select" label="Mode">
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41 <option value="geno">Genome</option>
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42 <option value="tran">Transcriptome</option>
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43 <option value="prot">Proteome</option>
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44 </param>
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45
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46 <param argument="--lineage_dataset" type="select" label="Lineage">
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47 <expand macro="lineages"/>
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48 </param>
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49
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50 <section name="adv" title="Advanced Options" expanded="False">
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51 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
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52 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
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53
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54 <conditional name="aug_prediction">
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55 <param name="augustus_mode" type="select" label="Augustus species model">
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56 <option value="no" selected="true">Use the default species for selected lineage</option>
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57 <option value="builtin">Use another predefined species model</option>
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58 <option value="history">Use a custom species model</option>
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59 </param>
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60 <when value="no"/>
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61 <when value="history">
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62 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
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63 </when>
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64 <when value="builtin">
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65 <param name="augustus_species" type="select" label="Augustus species model">
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66 <expand macro="augustus_species"/>
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67 </param>
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68 </when>
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69 </conditional>
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70 <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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71 </section>
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72 </inputs>
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73 <outputs>
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74 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"/>
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75 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
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76 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"/>
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77 </outputs>
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78 <tests>
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79 <test>
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80 <param name="input" value="genome.fa"/>
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81 <param name="lineage_dataset" value="arthropoda_odb10"/>
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82 <param name="mode" value="geno"/>
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83 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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84 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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85 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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86 </test>
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87 <test>
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88 <param name="input" value="proteome.fa"/>
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89 <param name="lineage_dataset" value="arthropoda_odb10"/>
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90 <param name="mode" value="prot"/>
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91 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
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92 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
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93 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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94 </test>
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95 <test>
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96 <param name="input" value="transcriptome.fa"/>
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97 <param name="lineage_dataset" value="arthropoda_odb10"/>
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98 <param name="mode" value="tran"/>
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99 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
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100 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
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101 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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102 </test>
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103 <test>
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104 <param name="input" value="genome.fa"/>
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105 <param name="lineage_dataset" value="arthropoda_odb10"/>
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106 <param name="mode" value="geno"/>
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107 <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
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108 <param name="adv|aug_prediction|augustus_species" value="human"/>
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109 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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110 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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111 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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112 </test>
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113 <test>
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114 <param name="input" value="genome.fa"/>
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115 <param name="lineage_dataset" value="arthropoda_odb10"/>
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116 <param name="mode" value="geno"/>
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117 <param name="adv|aug_prediction|augustus_mode" value="history"/>
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118 <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
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119 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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120 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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121 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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122 </test>
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123 </tests>
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124 <help>
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125 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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126
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127 .. _BUSCO: http://busco.ezlab.org/
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128 </help>
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129 <expand macro="citations"/>
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130 </tool>