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1 <tool id="augustus" name="Augustus" version="0.3.1">
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2 <description>gene prediction for eukaryotic genomes</description>
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3 <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.7">augustus</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <regex match="Error:" />
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11 <regex match="Exception:" />
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12 </stdio>
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13 <command>
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14 <![CDATA[
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15 ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
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16 ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed
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17 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files
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18
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19 augustus
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20 --strand=$strand
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21 $noInFrameStop
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22 $gff
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23
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24 #if 'protein' in str($outputs).split(','):
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25 --protein=on
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26 #else:
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27 --protein=off
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28 #end if
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29
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30 #if 'codingseq' in str($outputs).split(','):
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31 --codingseq=on
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32 #else:
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33 --codingseq=off
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34 #end if
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35
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36 #if 'introns' in str($outputs).split(','):
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37 --introns=on
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38 #else:
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39 --introns=off
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40 #end if
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41
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42 #if 'start' in str($outputs).split(','):
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43 --start=on
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44 #else:
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45 --stop=off
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46 #end if
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47
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48 #if 'stop' in str($outputs).split(','):
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49 --stop=on
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50 #else:
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51 --stop=off
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52 #end if
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53
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54 #if 'cds' in str($outputs).split(','):
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55 --cds=on
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56 #else:
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57 --cds=off
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58 #end if
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59
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60 $singlestrand
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61 $input_genome
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62 $mea
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63 $utr
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64 --genemodel=$genemodel
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65 --species=$organism
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66 ##--outfile=$output
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67 | tee $output
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68 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
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69 | python $__tool_directory__/extract_features.py
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70 #if 'protein' in str($outputs).split(','):
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71 --protein $protein_output
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72 #end if
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73 #if 'codingseq' in str($outputs).split(','):
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74 --codingseq $codingseq_output
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75 #end if
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76 #end if
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77 ]]>
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78 </command>
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79 <inputs>
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80 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
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81 <param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons (--noInFrameStop)" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur" />
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82 <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands (--singlestrand)" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
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83 <param name="mea" type="boolean" label="Using the maximum expected accuracy approach (--mea)" truevalue="--mea=1" falsevalue="" checked="false" help="MEA is an alternative decoding approach." />
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84 <param name="utr" type="boolean" label="Predict the untranslated regions in addition to the coding sequence (--UTR)" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
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85
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86 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
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87 <option value="human">Homo sapiens</option>
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88 <option value="fly">Drosophila melanogaster</option>
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89 <option value="arabidopsis">Arabidopsis thaliana</option>
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90 <option value="brugia ">Brugia malayi</option>
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91 <option value="aedes">Aedes aegypti</option>
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92 <option value="tribolium2012">Tribolium castaneum</option>
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93 <option value="schistosoma">Schistosoma mansoni</option>
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94 <option value="tetrahymena">Tetrahymena thermophila</option>
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95 <option value="galdieria">Galdieria sulphuraria</option>
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96 <option value="maize">Zea mays</option>
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97 <option value="toxoplasma ">Toxoplasma gondii</option>
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98 <option value="caenorhabditis ">Caenorhabditis elegans</option>
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99 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
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100 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
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101 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
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102 <option value="aspergillus_terreus">Aspergillus terreus</option>
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103 <option value="botrytis_cinerea ">Botrytis cinerea</option>
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104 <option value="candida_albicans ">Candida albicans</option>
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105 <option value="candida_guilliermondii ">Candida guilliermondii</option>
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106 <option value="candida_tropicalis ">Candida tropicalis</option>
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107 <option value="chaetomium_globosum">Chaetomium globosum</option>
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108 <option value="coccidioides_immitis ">Coccidioides immitis</option>
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109 <option value="coprinus ">Coprinus cinereus</option>
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110 <option value="coprinus_cinereus">Coprinus cinereus</option>
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111 <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option>
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112 <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option>
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113 <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option>
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114 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
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115 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
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116 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
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117 <option value="fusarium_graminearum ">Fusarium graminearum</option>
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118 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
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119 <option value="(histoplasma)">Histoplasma capsulatum</option>
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120 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
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121 <option value="laccaria_bicolor ">Laccaria bicolor</option>
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122 <option value="lamprey">Petromyzon marinus</option>
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123 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
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124 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
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125 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
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126 <option value="neurospora_crassa">Neurospora crassa</option>
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127 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
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128 <option value="pichia_stipitis">Pichia stipitis</option>
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129 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
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130 <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option>
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131 <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option>
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132 <option value="(saccharomyces)">Saccharomyces cerevisiae</option>
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133 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
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134 <option value="trichinella">Trichinella spiralis</option>
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135 <option value="ustilago_maydis">Ustilago maydis</option>
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136 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
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137 <option value="nasonia">Nasonia vitripennis</option>
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138 <option value="tomato">Solanum lycopersicum</option>
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139 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
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140 <option value="amphimedon">Amphimedon queenslandica</option>
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141 <option value="pneumocystis">Pneumocystis jirovecii</option>
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142 <option value="chicken">Gallus gallus domesticus (chicken)</option>
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143 <option value="cacao">Theobroma cacao (cacao)</option>
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144 <option value="heliconius_melpomene1">Heliconius melpomene</option>
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145 <option value="xenoturbella">Xenoturbella</option>
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146 </param>
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147
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148 <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand.">
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149 <option value="both">both</option>
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150 <option value="forward">forward</option>
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151 <option value="backward">backward</option>
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152 </param>
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153
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154 <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help.">
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155 <option value="complete">complete</option>
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156 <option value="partial">partial</option>
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157 <option value="intronless">intronless</option>
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158 <option value="atleastone">atleastone</option>
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159 <option value="exactlyone">exactlyone</option>
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160 <option value="bacterium">bacterium (beta version)</option>
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161 </param>
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162
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163
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164 <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
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165
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166 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
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167 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
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168 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
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169 <option value="introns">predicted intron sequences (--introns)</option>
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170 <option value="start">predicted start codons (--start)</option>
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171 <option value="stop">predicted stop codons (--stop)</option>
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172 <option value="cds" selected="true">CDS region (--cds)</option>
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173
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174 <validator type="no_options" message="Please select at least one output file." />
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175 </param>
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176
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177
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178 </inputs>
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179 <outputs>
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180 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
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181 <change_format>
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182 <when input="gff" value="--gff3=on" format="gff" />
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183 </change_format>
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184 </data>
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185 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
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186 <filter>'protein' in outputs</filter>
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187 </data>
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188 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
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189 <filter>'codingseq' in outputs</filter>
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190 </data>
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191 </outputs>
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192 <tests>
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193 <test>
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194 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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195 <param name="organism" value="human" />
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196 <param name="utr" value="--UTR=on" />
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197 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/>
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198 </test>
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199 <test>
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200 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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201 <param name="organism" value="human" />
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202 <param name="utr" value="--UTR=on" />
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203 <param name="gff" value="--gff3=on" />
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204 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/>
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205 </test>
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206 <test>
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207 <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
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208 <param name="organism" value="arabidopsis" />
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209 <param name="singlestrand" value="--singlestrand=true" />
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210 <param name="mea" value="--mea=1" />
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211 <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>
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212 </test>
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213 <test>
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214 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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215 <param name="organism" value="human" />
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216 <param name="outputs" value="protein,codingseq,introns,cds" />
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217 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>
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218 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
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219 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
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220 </test>
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221 </tests>
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222 <help>
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223 <![CDATA[
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224
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225 **What it does**
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226
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227 AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
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228 It can be used as an ab initio program, which means it bases its prediction purely on the
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229 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
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230 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
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231
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232 -----
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233
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234 **Parameters**
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235
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236 Gene Model::
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237
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238 partial : allow prediction of incomplete genes at the sequence boundaries (default)
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239 intronless : only predict single-exon genes like in prokaryotes and some eukaryotes
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240 complete : only predict complete genes
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241 atleastone : predict at least one complete gene
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242 exactlyone : predict exactly one complete gene
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243
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244
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245
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246 **Example**
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247
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248 Suppose you have the following DNA formatted sequences::
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249
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250 >Seq1
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251 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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252 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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253 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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254 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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255 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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256
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257 Running this tool will produce this::
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258
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259 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
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260 #
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261 # Constraints/Hints:
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262 # (none)
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263 # Predicted genes for sequence number 1 on both strands
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264 # start gene g1
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265 scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
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266 scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
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267 scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
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268 scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
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269 scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
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270 scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
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271 scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
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272 scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
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273 scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
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274 scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
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275 scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
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276 scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
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277 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
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278 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
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279 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
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280
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281
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282 ]]>
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283 </help>
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284 <citations>
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285 <citation type="doi">10.1093/bioinformatics/btg1080</citation>
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286 </citations>
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287 </tool>
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