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annotate augustus.xml @ 15:912f9476dec8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Mon, 30 Aug 2021 21:43:05 +0000
parents 66c8e9d8d1c4
children 22127ef4695b
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66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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1 <tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@">
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2 <description>gene prediction for prokaryotic and eukaryotic genomes</description>
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3 <xrefs>
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4 <xref type="bio.tools">augustus</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 #if $model.augustus_mode == 'history'
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14 ## Using an augustus model from history, we need to unzip it and let augustus find it
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48528e640fe6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
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16 cp -r `command -v augustus | xargs dirname`/../config/ augustus_dir/ &&
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18 mkdir -p 'augustus_dir/species/' &&
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20 tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null &&
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22 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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23 #end if
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24
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25 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
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26 ## script is used to extract the sequences into additional files
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27
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28 augustus
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29 --strand=$strand
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30 $noInFrameStop
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31 $gff
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32 --uniqueGeneId=true
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33
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34 #if 'protein' in str($outputs).split(','):
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35 --protein=on
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36 #else:
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37 --protein=off
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38 #end if
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39
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40 #if 'codingseq' in str($outputs).split(','):
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41 --codingseq=on
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42 #else:
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43 --codingseq=off
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44 #end if
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45
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46 #if 'introns' in str($outputs).split(','):
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47 --introns=on
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48 #else:
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49 --introns=off
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50 #end if
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51
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52 #if 'start' in str($outputs).split(','):
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53 --start=on
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54 #else:
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55 --stop=off
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56 #end if
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57
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58 #if 'stop' in str($outputs).split(','):
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59 --stop=on
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60 #else:
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61 --stop=off
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62 #end if
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63
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64 #if 'cds' in str($outputs).split(','):
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65 --cds=on
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66 #else:
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67 --cds=off
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68 #end if
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69
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70 $singlestrand
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71 $input_genome
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72 $utr
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73 --genemodel=$genemodel
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74 --softmasking=$softmasking
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75 #if $hints.usehints == 'T'
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76 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
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77 #end if
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79 #if $range.userange == 'T'
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80 --predictionStart=$range.start --predictionEnd=$range.stop
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81 #end if
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82
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83 #if $model.augustus_mode == 'history'
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84 --species=local
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85 #else
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86 --species=$model.organism
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87 #end if
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89 | tee '$output'
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90 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
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91 | python $__tool_directory__/extract_features.py
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92 #if 'protein' in str($outputs).split(','):
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93 --protein $protein_output
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94 #end if
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95 #if 'codingseq' in str($outputs).split(','):
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96 --codingseq $codingseq_output
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97 #end if
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98 #end if
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99 ]]>
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100 </command>
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101 <inputs>
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102 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
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103 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"
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104 label="Don't report transcripts with in-frame stop codons"
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105 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
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106 help="Otherwise, intron-spanning stop codons could occur." />
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107 <param name="singlestrand" type="boolean" argument="--singlestrand"
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108 label="Predict genes independently on each strand"
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109 help="This allows overlapping genes on opposite strands."
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110 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
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111
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112 <param name="utr" type="boolean" argument="--UTR"
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113 label="Predict the untranslated regions in addition to the coding sequence"
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114 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
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115 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
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116
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117
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118 <conditional name="model">
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119 <param name="augustus_mode" type="select" label="Trainingset">
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120 <option value="builtin">Run Augustus with a predefined trainingset</option>
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121 <option value="history">Run Augustus with a custom trainingset</option>
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122 </param>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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123 <when value="history">
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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124 <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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125 </when>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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126 <when value="builtin">
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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127 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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128 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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129 <option value="human">Homo sapiens</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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130 <option value="fly">Drosophila melanogaster</option>
13
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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131 <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option>
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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132 <option value="arabidopsis">Arabidopsis thaliana</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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133 <option value="brugia ">Brugia malayi</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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134 <option value="aedes">Aedes aegypti</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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135 <option value="tribolium2012">Tribolium castaneum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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136 <option value="schistosoma">Schistosoma mansoni</option>
13
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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137 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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138 <option value="tetrahymena">Tetrahymena thermophila</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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139 <option value="galdieria">Galdieria sulphuraria</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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140 <option value="maize">Zea mays</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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141 <option value="toxoplasma">Toxoplasma gondii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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142 <option value="caenorhabditis ">Caenorhabditis elegans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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143 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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144 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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145 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
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146 <option value="aspergillus_terreus">Aspergillus terreus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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147 <option value="botrytis_cinerea ">Botrytis cinerea</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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148 <option value="candida_albicans ">Candida albicans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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149 <option value="candida_guilliermondii ">Candida guilliermondii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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150 <option value="candida_tropicalis ">Candida tropicalis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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151 <option value="chaetomium_globosum">Chaetomium globosum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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152 <option value="coccidioides_immitis">Coccidioides immitis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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153 <option value="coprinus">Coprinus cinereus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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154 <option value="coprinus_cinereus">Coprinus cinereus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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155 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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156 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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157 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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158 <option value="cryptococcus">Cryptococcus neoformans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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159 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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160 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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161 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
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162 <option value="fusarium_graminearum ">Fusarium graminearum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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163 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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164 <option value="histoplasma">Histoplasma capsulatum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
165 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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166 <option value="laccaria_bicolor ">Laccaria bicolor</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
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167 <option value="lamprey">Petromyzon marinus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
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168 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
diff changeset
169 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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170 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
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diff changeset
171 <option value="neurospora_crassa">Neurospora crassa</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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172 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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173 <option value="pichia_stipitis">Pichia stipitis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
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174 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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175 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
176 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
177 <option value="saccharomyces">Saccharomyces cerevisiae</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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178 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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179 <option value="trichinella">Trichinella spiralis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
180 <option value="ustilago_maydis">Ustilago maydis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
181 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
182 <option value="nasonia">Nasonia vitripennis</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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183 <option value="tomato">Solanum lycopersicum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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184 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
185 <option value="amphimedon">Amphimedon queenslandica</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
186 <option value="pneumocystis">Pneumocystis jirovecii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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187 <option value="chicken">Gallus gallus domesticus (chicken)</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
188 <option value="cacao">Theobroma cacao (cacao)</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
189 <option value="heliconius_melpomene1">Heliconius melpomene</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
190 <option value="xenoturbella">Xenoturbella</option>
13
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
191 <option value="E_coli_K12">Escherichia coli K12</option>
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
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192 <option value="c_elegans_trsk">c elegans trsk</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
193 <option value="camponotus_floridanus">Camponotus floridanus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
194 <option value="coyote_tobacco">Coyote tobacco</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
195 <option value="s_aureus">Staphylococcus aureus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
196 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
13
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
197 <option value="wheat">Triticum aestivum</option>
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
198 <option value="zebrafish">Danio rerio</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
199 <option value="anidulans">Aspergillus nidulans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
200 <option value="bombus_impatiens1">Bombus impatiens1</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
201 <option value="bombus_terrestris2">Bombus terrestris2</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
202 <option value="botrytis_cinerea">Botrytis cinerea</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
203 <option value="brugia_malayi">Brugia malayi</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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204 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
205 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
206 <option value="culex_pipiens">Culex pipiens</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
207 <option value="elephant_shark">Callorhinchus milii</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
208 <option value="honeybee1">Apis mellifera</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
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209 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
bgruening
parents: 9
diff changeset
210 <option value="pea_aphid">Acyrthosiphon pisum</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
diff changeset
211 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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parents: 9
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212 <option value="ustilago_maydis">Ustilago maydis</option>
13
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
213 <option value="verticillium_albo_atrum1">Verticillium albo-atrum</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
214 <option value="verticillium_longisporum1">Verticillium longisporum</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
215 <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
216 <option value="adorsata">Apis dorsata</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
217 <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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218 <option value="maker2_athal1">Arabidopsis thaliana (maker2_athal1)</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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219 <option value="maker2_c_elegans1">Caenorhabditis elegans (maker2_c_elegans1)</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
220 <option value="maker2_spomb1">Saccharomyces cerevisiae (maker2_spomb1)</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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221 <option value="parasteatoda">Parasteatoda SP.</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
diff changeset
222 <option value="rice">Oryza sp.</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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223 <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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224 <option value="Ptychodera_flava">Ptychodera flava</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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225 <option value="Argopecten_irridians">Argopecten irridians</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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226 <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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227 <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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228 <option value="Chrysaora_chesapeakeij">Chrysaora chesapeakeij</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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229 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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230 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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231 <option value="Aurelia_aurita">Aurelia aurita</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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232 <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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233 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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234 <option value="Gonapodya_prolifera">Dunaliella salina</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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235 <option value="Sordaria_macrospora">Sordaria macrospora</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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236 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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237 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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238 <option value="Monoraphidium_neglectum">Monoraphidium_neglectum</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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239 <option value="Raphidocelis_subcapita">Raphidocelis subcapita</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 12
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240 <option value="Ostreococcus_tauri">Ostreococcus tauri</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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241 <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp. lucimarinus</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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242 <option value="Micromonas_pusilla">Micromonas pusilla</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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243 <option value="Micromonas_commoda">Micromonas commoda</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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244 <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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245 <option value="Thalassiosira_pseudonana">Thalassiosira pseudonana</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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246 <option value="Pseudo-nitzschia_multistriata">Pseudo-nitzschia multistriata</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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247 <option value="Phaeodactylum_tricornutum">Phaeodactylum tricornutum</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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248 <option value="Fragilariopsis_cylindrus">Fragilariopsis cylindrus</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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249 <option value="Fistulifera_solaris">Fistulifera solaris</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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250 <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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251 <option value="Chloropicon_primus">Chloropicon primus</option>
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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252 </param>
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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253 </when>
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254 </conditional>
0
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255
13
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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256 <param name="softmasking" type="boolean" argument="--softmasking"
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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257 label="Softmasking"
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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258 truevalue="1" falsevalue="0" checked="true"
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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259 help="If this option is enabled, lowercase letters are considered as repeated regions." />
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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260
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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261
9
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iuc
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262 <param name="strand" type="select" argument="--strand"
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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263 label="Predict genes on specific strands">
0
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264 <option value="both">both</option>
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265 <option value="forward">forward</option>
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266 <option value="backward">backward</option>
9
4611e8073293 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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267 </param>
0
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268
9
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269 <param name="genemodel" label="Gene Model" type="select"
11
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270 help="Gene Model to predict, for more information please refer to the help.">
0
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271 <option value="complete">complete</option>
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272 <option value="partial">partial</option>
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273 <option value="intronless">intronless</option>
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274 <option value="atleastone">atleastone</option>
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275 <option value="exactlyone">exactlyone</option>
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276 </param>
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277
11
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278 <conditional name="hints">
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279 <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
e519d7b4f9ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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280 <option value="F">No</option>
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iuc
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281 <option value="T">Yes</option>
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282 </param>
e519d7b4f9ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
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283 <when value="T">
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iuc
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284 <param name="hintsfile" label="Select hints file from history" type="data" format="gff"
e519d7b4f9ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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285 help="A file containing hints in gff format (--hintsfile)"/>
e519d7b4f9ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
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286 <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt"
e519d7b4f9ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
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287 help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/>
e519d7b4f9ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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288 </when>
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289 <when value="F">
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290 </when>
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291 </conditional>
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292
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293 <conditional name="range">
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294 <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
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295 <option value="F">No</option>
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296 <option value="T">Yes</option>
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297 </param>
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298 <when value="T">
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299 <param name="start" label="Starting position" type="integer" value=""
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300 help="The beginning of the search range (--predictionStart)"/>
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301 <param name="stop" label="Ending position" type="integer" value=""
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302 help="The end of the search range (--predictionEnd); must be greater than starting position"/>
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303 </when>
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304 <when value="F">
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305 </when>
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306 </conditional>
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307
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308 <param name="gff" type="boolean" label="GFF formated output"
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309 help="Standard output is GTF."
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310 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
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311
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312 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
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313 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
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314 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
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315 <option value="introns">predicted intron sequences (--introns)</option>
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316 <option value="start">predicted start codons (--start)</option>
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317 <option value="stop">predicted stop codons (--stop)</option>
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318 <option value="cds" selected="true">CDS region (--cds)</option>
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319 </param>
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320 </inputs>
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321 <outputs>
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322 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
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323 <change_format>
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324 <when input="gff" value="--gff3=on" format="gff3" />
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325 </change_format>
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326 </data>
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327 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
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328 <filter>'protein' in outputs</filter>
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329 </data>
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330 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
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331 <filter>'codingseq' in outputs</filter>
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332 </data>
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333 </outputs>
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334 <tests>
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335 <test>
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336 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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337 <param name="organism" value="human" />
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338 <param name="utr" value="True" />
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339 <param name="softmasking" value="False"/>
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340 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
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341 </test>
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342 <test>
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343 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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344 <param name="organism" value="human" />
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345 <param name="utr" value="True" />
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346 <param name="gff" value="True" />
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347 <param name="softmasking" value="False"/>
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348 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
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349 </test>
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350 <test>
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351 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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352 <param name="organism" value="human" />
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353 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
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354 <param name="softmasking" value="False"/>
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355 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
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356 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
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357 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
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358 </test>
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359 <test>
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360 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
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361 <param name="organism" value="fly" />
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362 <param name="usehints" value="T" />
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363 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
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364 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
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365 <param name="outputs" value="" />
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366 <param name="softmasking" value="False"/>
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367 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
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368 <assert_contents>
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369 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
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370 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
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371 </assert_contents>
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372 </output>
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373
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374 </test>
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375 <test>
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376 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
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377 <param name="organism" value="fly" />
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378 <param name="usehints" value="T" />
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379 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
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380 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
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381 <param name="userange" value="T" />
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382 <param name="start" value="7000" />
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383 <param name="stop" value="9000" />
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384 <param name="outputs" value="" />
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385 <param name="softmasking" value="False"/>
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386 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
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387 <assert_contents>
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388 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
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389 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
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390 </assert_contents>
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391 </output>
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392 </test>
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393 <!-- Test softmasking parameter-->
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394 <test>
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395 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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396 <param name="organism" value="human" />
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397 <param name="utr" value="True" />
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398 <param name="softmasking" value="True"/>
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399 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
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400 </test>
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401
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402 </tests>
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403 <help>
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404 <![CDATA[
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405
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406 **What it does**
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407
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408 AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller.
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409 It can be used as an ab initio program, which means it bases its prediction purely on the
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410 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
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411 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
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412
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413
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414 **Input**
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415
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416 Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence.
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417
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418
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419 **Output**
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420
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421 Augustus produces three output files: a FASTA file with predicted coding sequences, a FASTA file with predicted protein sequences and a gtf/GFF output file if selected.
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422
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423
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424 **Parameters**
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425
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426 Gene Model:
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427
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428 partial: allow prediction of incomplete genes at the sequence boundaries (default)
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429 intronless: only predict single-exon genes like in prokaryotes and some eukaryotes
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430 complete: only predict complete genes
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431 atleastone: predict at least one complete gene
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432 exactlyone: predict exactly one complete gene
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433
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434
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435
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436 **Example**
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437
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438 Suppose you have the following DNA FASTA sequence:
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439
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440 >Seq1
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441 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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442 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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443 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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444 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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445 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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446
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447
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448 Running this tool will produce this:
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449
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450 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
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451 #
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452 # Constraints/Hints:
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453 # (none)
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454 # Predicted genes for sequence number 1 on both strands
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455 # start gene g1
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456 scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
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457 scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
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458 scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
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459 scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
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460 scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
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461 scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
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462 scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
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463 scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
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464 scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
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465 scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
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466 scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
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467 scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
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468 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
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469 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
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470 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
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471
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472
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473 ]]>
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474 </help>
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475 <expand macro="citations"/>
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476 </tool>