annotate augustus.xml @ 4:4de31938431b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Fri, 20 Oct 2017 03:48:57 -0400
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1 <tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@">
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2 <description>gene prediction for prokaryotic and eukaryotic genomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="aggressive">
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8 <![CDATA[
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9 #if $model.augustus_mode == 'history'
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11 ## Using an augustus model from history, we need to unzip it and let augustus find it
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13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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15 mkdir -p 'augustus_dir/species/' &&
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17 tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null &&
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19 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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20 #end if
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22 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
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23 ## script is used to extract the sequences into additional files
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24
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25 augustus
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26 --strand=$strand
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27 $noInFrameStop
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28 $gff
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29 --uniqueGeneId=true
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30
1
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31 #if 'protein' in str($outputs).split(','):
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32 --protein=on
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33 #else:
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34 --protein=off
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35 #end if
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36
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37 #if 'codingseq' in str($outputs).split(','):
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38 --codingseq=on
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39 #else:
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40 --codingseq=off
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41 #end if
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42
1
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43 #if 'introns' in str($outputs).split(','):
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44 --introns=on
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45 #else:
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46 --introns=off
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47 #end if
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48
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49 #if 'start' in str($outputs).split(','):
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50 --start=on
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51 #else:
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52 --stop=off
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53 #end if
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54
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55 #if 'stop' in str($outputs).split(','):
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56 --stop=on
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57 #else:
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58 --stop=off
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59 #end if
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60
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61 #if 'cds' in str($outputs).split(','):
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62 --cds=on
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63 #else:
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64 --cds=off
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65 #end if
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66
0
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67 $singlestrand
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68 $input_genome
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69 $utr
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70 --genemodel=$genemodel
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72
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73 #if $model.augustus_mode == 'history'
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74 --species=local
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75 #else
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76 --species=$model.organism
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77 #end if
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79 | tee '$output'
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80 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
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81 | python $__tool_directory__/extract_features.py
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82 #if 'protein' in str($outputs).split(','):
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83 --protein $protein_output
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84 #end if
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85 #if 'codingseq' in str($outputs).split(','):
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86 --codingseq $codingseq_output
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87 #end if
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88 #end if
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89 ]]>
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90 </command>
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91 <inputs>
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92 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
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93 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"
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94 label="Don't report transcripts with in-frame stop codons"
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95 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
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96 help="Otherwise, intron-spanning stop codons could occur." />
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97 <param name="singlestrand" type="boolean" argument="--singlestrand"
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98 label="Predict genes independently on each strand"
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99 help="This allows overlapping genes on opposite strands."
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100 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
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101
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102 <param name="utr" type="boolean" argument="--UTR"
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103 label="Predict the untranslated regions in addition to the coding sequence"
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104 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
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105 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
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106
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107
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108 <conditional name="model">
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109 <param name="augustus_mode" type="select" label="Trainingset">
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110 <option value="builtin">Run Augustus with a predefined trainingset</option>
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111 <option value="history">Run Augustus with a custom trainingset</option>
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112 </param>
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113 <when value="history">
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114 <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
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115 </when>
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116 <when value="builtin">
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117 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
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118 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
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119 <option value="human">Homo sapiens</option>
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120 <option value="fly">Drosophila melanogaster</option>
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121 <option value="arabidopsis">Arabidopsis thaliana</option>
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122 <option value="brugia ">Brugia malayi</option>
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123 <option value="aedes">Aedes aegypti</option>
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124 <option value="tribolium2012">Tribolium castaneum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
125 <option value="schistosoma">Schistosoma mansoni</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
126 <option value="tetrahymena">Tetrahymena thermophila</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
127 <option value="galdieria">Galdieria sulphuraria</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
128 <option value="maize">Zea mays</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
129 <option value="toxoplasma">Toxoplasma gondii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
130 <option value="caenorhabditis ">Caenorhabditis elegans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
131 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
132 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
133 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
134 <option value="aspergillus_terreus">Aspergillus terreus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
135 <option value="botrytis_cinerea ">Botrytis cinerea</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
136 <option value="candida_albicans ">Candida albicans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
137 <option value="candida_guilliermondii ">Candida guilliermondii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
138 <option value="candida_tropicalis ">Candida tropicalis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
139 <option value="chaetomium_globosum">Chaetomium globosum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
140 <option value="coccidioides_immitis">Coccidioides immitis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
141 <option value="coprinus">Coprinus cinereus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
142 <option value="coprinus_cinereus">Coprinus cinereus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
143 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
144 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
145 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
146 <option value="cryptococcus">Cryptococcus neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
147 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
148 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
149 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
150 <option value="fusarium_graminearum ">Fusarium graminearum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
151 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
152 <option value="histoplasma">Histoplasma capsulatum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
153 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
154 <option value="laccaria_bicolor ">Laccaria bicolor</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
155 <option value="lamprey">Petromyzon marinus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
156 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
157 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
158 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
159 <option value="neurospora_crassa">Neurospora crassa</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
160 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
161 <option value="pichia_stipitis">Pichia stipitis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
162 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
163 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
164 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
165 <option value="saccharomyces">Saccharomyces cerevisiae</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
166 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
167 <option value="trichinella">Trichinella spiralis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
168 <option value="ustilago_maydis">Ustilago maydis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
169 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
170 <option value="nasonia">Nasonia vitripennis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
171 <option value="tomato">Solanum lycopersicum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
172 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
173 <option value="amphimedon">Amphimedon queenslandica</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
174 <option value="pneumocystis">Pneumocystis jirovecii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
175 <option value="chicken">Gallus gallus domesticus (chicken)</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
176 <option value="cacao">Theobroma cacao (cacao)</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
177 <option value="heliconius_melpomene1">Heliconius melpomene</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
178 <option value="xenoturbella">Xenoturbella</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
179 <option value="E_coli_K12">E coli K12</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
180 <option value="c_elegans_trsk">c elegans trsk</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
181 <option value="camponotus_floridanus">Camponotus floridanus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
182 <option value="coyote_tobacco">Coyote tobacco</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
183 <option value="s_aureus">Staphylococcus aureus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
184 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
185 <option value="wheat">wheat</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
186 <option value="zebrafish">Danio rerio</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
187 <option value="anidulans">Aspergillus nidulans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
188 <option value="bombus_impatiens1">Bombus impatiens1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
189 <option value="bombus_terrestris2">Bombus terrestris2</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
190 <option value="botrytis_cinerea">Botrytis cinerea</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
191 <option value="brugia_malayi">Brugia malayi</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
192 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
193 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
194 <option value="culex_pipiens">Culex pipiens</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
195 <option value="elephant_shark">Callorhinchus milii</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
196 <option value="honeybee1">Apis mellifera</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
197 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
198 <option value="pea_aphid">Acyrthosiphon pisum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
199 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
200 <option value="ustilago_maydis">Ustilago maydis</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
201 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
202 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
203 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
204 <option value="adorsata">adorsata</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
205 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
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206 <option value="maker2_athal1">maker2_athal1</option>
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207 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
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208 <option value="maker2_dmel1">maker2_dmel1</option>
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209 <option value="maker2_spomb1">maker2_spomb1</option>
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210 <option value="parasteatoda">parasteatoda</option>
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211 <option value="rice">rice</option>
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212 <option value="schistosoma2">schistosoma2</option>
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213 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
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214 </param>
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215 </when>
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216 </conditional>
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217
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218 <param name="strand" type="select" argument="--strand"
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219 label="Predict genes on specific strands">
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220 <option value="both">both</option>
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221 <option value="forward">forward</option>
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222 <option value="backward">backward</option>
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223 </param>
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224
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225 <param name="genemodel" label="Gene Model" type="select"
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226 help="Gene Model to predict, for more information please refere to the help.">
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227 <option value="complete">complete</option>
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228 <option value="partial">partial</option>
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229 <option value="intronless">intronless</option>
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230 <option value="atleastone">atleastone</option>
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231 <option value="exactlyone">exactlyone</option>
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232 </param>
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233
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234 <param name="gff" type="boolean" label="GFF formated output"
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235 help="Standard output is GTF."
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236 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
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237
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238 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
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239 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
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240 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
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241 <option value="introns">predicted intron sequences (--introns)</option>
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242 <option value="start">predicted start codons (--start)</option>
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243 <option value="stop">predicted stop codons (--stop)</option>
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244 <option value="cds" selected="true">CDS region (--cds)</option>
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245 </param>
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246 </inputs>
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247 <outputs>
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248 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
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249 <change_format>
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250 <when input="gff" value="--gff3=on" format="gff3" />
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251 </change_format>
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252 </data>
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253 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
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254 <filter>'protein' in outputs</filter>
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255 </data>
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256 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
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257 <filter>'codingseq' in outputs</filter>
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258 </data>
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259 </outputs>
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260 <tests>
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261 <test>
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262 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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263 <param name="organism" value="human" />
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264 <param name="utr" value="True" />
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265 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
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266 </test>
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267 <test>
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268 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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269 <param name="organism" value="human" />
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270 <param name="utr" value="True" />
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271 <param name="gff" value="True" />
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272 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
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273 </test>
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274 <test>
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275 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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276 <param name="organism" value="human" />
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277 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
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278 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
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279 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
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280 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
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281 </test>
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282 </tests>
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283 <help>
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284 <![CDATA[
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285
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286 **What it does**
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287
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288 AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller.
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289 It can be used as an ab initio program, which means it bases its prediction purely on the
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290 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
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291 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
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292
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293
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294 **Input**
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295
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296 Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence.
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297
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298
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299 **Output**
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300
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301 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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302
0
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303
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304 **Parameters**
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305
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306 Gene Model:
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307
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308 partial: allow prediction of incomplete genes at the sequence boundaries (default)
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309 intronless: only predict single-exon genes like in prokaryotes and some eukaryotes
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310 complete: only predict complete genes
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311 atleastone: predict at least one complete gene
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312 exactlyone: predict exactly one complete gene
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313
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314
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315
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316 **Example**
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317
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318 Suppose you have the following DNA FASTA sequence:
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319
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320 >Seq1
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321 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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322 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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323 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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324 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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325 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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326
4
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327
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328 Running this tool will produce this:
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329
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330 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
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331 #
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332 # Constraints/Hints:
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333 # (none)
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334 # Predicted genes for sequence number 1 on both strands
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335 # start gene g1
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336 scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
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337 scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
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338 scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
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339 scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
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340 scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
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341 scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
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342 scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
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343 scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
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344 scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
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345 scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
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346 scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
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347 scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
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348 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
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349 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
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350 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
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351
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352
2
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353 ]]>
0
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354 </help>
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
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355 <expand macro="citations"/>
0
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356 </tool>