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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
author iuc
date Thu, 17 Jul 2025 09:06:01 +0000
parents 0fc0f9cf035a
children
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1 <tool id="augustus" name="Augustus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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 <xrefs>
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7 <xref type="bio.tools">augustus</xref>
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8 </xrefs>
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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 $model.augustus_mode == 'history'
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14 ## Using an augustus model from history, we need to unzip it and let augustus find it
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16 cp -r \$(dirname \$(command -v augustus))/../config/ augustus_dir/ &&
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18 mkdir -p 'augustus_dir/species/' &&
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20 tar -C 'augustus_dir/species/' -xzvf '$model.custom_model' > /dev/null &&
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22 export AUGUSTUS_CONFIG_PATH=./augustus_dir/ &&
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23 #end if
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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 #for arg in ['protein', 'codingseq', 'introns', 'start', 'stop', 'cds']
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35 #if arg in $outputs:
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36 --$arg=on
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37 #else
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38 --$arg=off
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39 #end if
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40 #end for
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41 $singlestrand
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42 '$input_genome'
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43 $utr
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44 --genemodel=$genemodel
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09855551d713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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45 --softmasking=$softmasking
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46 #if $hints.usehints == 'T'
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47 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
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48 #end if
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50 #if $range.userange == 'T'
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51 --predictionStart=$range.start --predictionEnd=$range.stop
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52 #end if
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54 #if $model.augustus_mode == 'history'
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55 --species=local
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56 #else
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57 --species=$model.organism
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58 #end if
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60 | tee '$output'
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61 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
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62 | python $__tool_directory__/extract_features.py
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63 #if 'protein' in str($outputs).split(','):
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64 --protein $protein_output
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65 #end if
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66 #if 'codingseq' in str($outputs).split(','):
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67 --codingseq $codingseq_output
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68 #end if
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69 #end if
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70 ]]>
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71 </command>
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72 <inputs>
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73 <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genome Sequence"/>
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74 <param argument="--noInFrameStop" type="boolean"
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75 label="Don't report transcripts with in-frame stop codons"
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76 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
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77 help="Otherwise, intron-spanning stop codons could occur." />
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78 <param type="boolean" argument="--singlestrand"
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79 label="Predict genes independently on each strand"
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80 help="This allows overlapping genes on opposite strands."
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81 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
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82
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83 <param name="utr" type="boolean" argument="--UTR"
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84 label="Predict the untranslated regions in addition to the coding sequence"
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85 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
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86 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
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87
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88
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89 <conditional name="model">
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90 <param name="augustus_mode" type="select" label="Trainingset">
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91 <option value="builtin">Run Augustus with a predefined trainingset</option>
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92 <option value="history">Run Augustus with a custom trainingset</option>
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93 </param>
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94 <when value="history">
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95 <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
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96 </when>
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97 <when value="builtin">
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98 <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="txt" help="Choose a specialised trainingset. If model name is different than species name it is shown in parentheses." >
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99 <!-- 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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100 <!-- Current list for AUGUSTUS (3.5.0) for i in $(ls ~/miniforge3/envs/__busco@5.8.0/config/species/); do echo \<option value=\"$i\"\>$(echo $i | sed 's/_/ /g')\</option\>; done -->
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
101 <option value="adorsata">Apis dorsata (adorsata)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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102 <option value="aedes">Aedes aegypti (aedes)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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103 <option value="amphimedon">Amphimedon queenslandica</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
104 <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
105 <option value="anidulans">Aspergillus nidulans (anidulans)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
106 <option value="Anopheles_gambiae">Anopheles gambiae</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
107 <option value="arabidopsis">Arabidopsis thaliana (arabidopsis)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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108 <option value="Argopecten_irradians">Argopecten irradians</option>
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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109 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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110 <option value="aspergillus_nidulans">Aspergillus nidulans</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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111 <option value="aspergillus_oryzae">Aspergillus oryzae</option>
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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112 <option value="aspergillus_terreus">Aspergillus terreus</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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113 <option value="Aurelia_aurita">Aurelia aurita</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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114 <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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115 <option value="Berviolum_minutum">Berviolum minutum</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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116 <option value="bombus_impatiens1">Bombus impatiens1</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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117 <option value="bombus_terrestris2">Bombus terrestris2</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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118 <option value="botrytis_cinerea">Botrytis cinerea</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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119 <option value="b_pseudomallei">Burkholderia pseudomallei (b_pseudomallei)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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120 <option value="Branchiostoma_floridae">Branchiostoma floridae</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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121 <option value="brugia">Brugia malayi (brugia)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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122 <option value="cacao">(cacao)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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123 <option value="caenorhabditis">Caenorhabditis elegans (caenorhabditis)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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124 <option value="camponotus_floridanus">Camponotus floridanus</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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125 <option value="candida_albicans">Candida albicans</option>
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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126 <option value="candida_guilliermondii">Candida guilliermondii</option>
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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127 <option value="candida_tropicalis">Candida tropicalis</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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128 <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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129 <!-- <option value="c_elegans_trsk">Caenorhabditis elegans</option> do not use according to augustus commit messages -->
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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130 <option value="chaetomium_globosum">Chaetomium globosum</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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131 <option value="chicken">Gallus gallus (chicken)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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132 <option value="chiloscyllium">Chiloscyllium punctatum (chiloscyllium)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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133 <option value="chlamy2011">chlamy2011</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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134 <option value="chlamydomonas">Chlamydomonas reinhardtii (chlamydomonas)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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135 <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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136 <option value="chlorella">chlorella</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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137 <option value="Chloropicon_primus">Chloropicon primus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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138 <option value="Chrysaora_chesapeakei">Chrysaora chesapeakei</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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139 <option value="ciona">ciona</option>
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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140 <option value="coccidioides_immitis">Coccidioides immitis</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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141 <option value="Conidiobolus_coronatus">Conidiobolus coronatus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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142 <option value="coprinus">coprinus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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143 <option value="coprinus_cinereus">Coprinus cinereus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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144 <option value="coyote_tobacco">Coyote tobacco</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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145 <option value="cryptococcus">cryptococcus</option>
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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146 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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147 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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148 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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149 <option value="Cryptosporidium_hominis">Cryptosporidium hominis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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150 <option value="culex">culex</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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151 <option value="Cyclotella_cryptica">Cyclotella cryptica</option>
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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152 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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153 <option value="Dermasterias_imbricata">Dermasterias imbricata</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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154 <option value="Dunaliella_salina">Dunaliella salina</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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155 <option value="E_coli_K12">Escherichia K12 (E_coli_K12)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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156 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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157 <option value="elephant_shark">Callorhinchus milii (elephant_shark)</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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158 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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159 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
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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160 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
161 <option value="Fistulifera_solaris">Fistulifera solaris</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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162 <option value="fly">Drosophila melanogaster (fly)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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163 <option value="fly_exp">Drosophila melanogaster (fly) experimental parameters</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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164 <option value="Fragilariopsis_cylindrus_CCMP1102">Fragilariopsis cylindrus CCMP1102</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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165 <option value="fusarium">fusarium</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
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166 <option value="fusarium_graminearum">Fusarium graminearum</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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167 <option value="galdieria">Galdieria sulphuraria (galdieria)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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168 <option value="generic">generic</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
169 <option value="gigaspora_margarita">Gigaspora margarita</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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170 <option value="Gonapodya_prolifera">Gonapodya prolifera</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
171 <option value="heliconius_melpomene1">Heliconius melpomene1</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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172 <option value="histoplasma">histoplasma</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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173 <option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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174 <option value="honeybee1">Apis mellifera (honeybee1)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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175 <option value="human">Homo sapiens (human)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
176 <option value="Hydra_vulgaris">Hydra vulgaris</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
177 <option value="hymenolepis_microstoma">Hymenolepis microstoma</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
178 <option value="japaneselamprey">Lethenteron camtschaticum (japaneselamprey)</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
diff changeset
179 <option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
diff changeset
180 <option value="laccaria_bicolor">Laccaria bicolor</option>
4
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="leishmania_tarentolae">Leishmania tarentolae</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
182 <option value="Leptasterias_sp">Leptasterias sp</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
183 <option value="Loa_loa">Loa loa</option>
4
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="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
9
bd0e53f3a891 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
iuc
parents: 7
diff changeset
185 <option value="magnaporthe_grisea">Magnaporthe grisea</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
186 <option value="maize">Zea mays (maize)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
187 <option value="maize5">Zea mays (maize5)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
188 <option value="Micromonas_commoda">Micromonas commoda</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
189 <option value="Micromonas_pusilla">Micromonas pusilla</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
190 <option value="mnemiopsis_leidyi">Mnemiopsis leidyi</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
191 <option value="Monoraphidium_neglectum">Monoraphidium neglectum</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
192 <option value="Monosiga_brevicollis">Monosiga brevicollis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
193 <option value="Naegleria_gruberi">Naegleria gruberi</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
194 <option value="nasonia">Nasonia vitripennis (nasonia)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
195 <option value="nematostella_vectensis">Nematostella vectensis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
196 <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
197 <option value="neurospora">neurospora</option>
4
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="neurospora_crassa">Neurospora crassa</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
199 <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
200 <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp lucimarinus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
201 <option value="Ostreococcus_tauri">Ostreococcus tauri</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
202 <option value="Paramecium_tetraurelia">Paramecium tetraurelia</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
203 <option value="parasteatoda">Parasteatoda tepidariorum (parasteatoda)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
204 <option value="pchrysosporium">Phanerochaete chrysosporium (pchrysosporium)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
205 <option value="pea_aphid">Acyrthosiphon pisum (pea_aphid)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
206 <option value="Pediculus_humanus">Pediculus humanus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
207 <option value="Perkinsus_marinus">Perkinsus marinus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
208 <option value="pfalciparum">Plasmodium falciparum (pfalciparum)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
209 <option value="Phaeodactylum_tricornutum">Phaeodactylum tricornutum</option>
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
210 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
211 <option value="Physcomitrium_patens">Physcomitrium patens</option>
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
212 <option value="pichia_stipitis">Pichia stipitis</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
213 <option value="pisaster">Pisaster ochraceus (pisaster)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
214 <option value="pneumocystis">pneumocystis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
215 <option value="Populus_trichocarpa">Populus trichocarpa</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
216 <option value="Pseudo-nitzschia_multistriata">Pseudo-nitzschia multistriata</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
217 <option value="Ptychodera_flava">Ptychodera flava</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
218 <option value="Pycnopodia_helianthoides">Pycnopodia helianthoides</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
219 <option value="Raphidocelis_subcapitata">Raphidocelis subcapitata</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
220 <option value="rhincodon">Rhincodon typus (rhincodon)</option>
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
221 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
222 <option value="rhodnius">Rhodnius</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
223 <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
224 <option value="rice">Oryza (rice)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
225 <option value="Ricinus_communis">Ricinus communis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
226 <option value="saccharomyces">Saccharomyces</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
227 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a 1</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
228 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
229 <option value="s_aureus">Staphylococcus aureus (s_aureus)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
230 <option value="schistosoma">Schistosoma mansoni (schistosoma)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
231 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 3
diff changeset
232 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
233 <option value="Sclerotinia_sclerotiorum">Sclerotinia sclerotiorum</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
234 <option value="scyliorhinus">Scyliorhinus torazame (scyliorhinus)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
235 <option value="sealamprey">Petromyzon marinus (sealamprey)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
236 <option value="Skeletonema_costatum">Skeletonema costatum</option>
7
09855551d713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 6
diff changeset
237 <option value="Sordaria_macrospora">Sordaria macrospora</option>
09855551d713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 6
diff changeset
238 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
11
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
239 <option value="s_pneumoniae">Streptococcus pneumoniae (s_pneumoniae)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
240 <option value="strongylocentrotus_purpuratus">Strongylocentrotus purpuratus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
241 <option value="sulfolobus_solfataricus">Sulfolobus solfataricus</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
242 <option value="sunflower">Helianthus annuus (sunflower)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
243 <option value="Taeniopygia_guttata">Taeniopygia guttata</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
244 <option value="template_prokaryotic">Template prokaryotic</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
245 <option value="tetrahymena">tetrahymena</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
246 <option value="Thalassiosira_pseudonana_CCMP1335">Thalassiosira pseudonana CCMP1335</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
247 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
248 <option value="tomato">Solanum lycopersicum (tomato)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
249 <option value="toxoplasma">Toxoplasma gondii (toxoplasma)</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
250 <option value="tribolium2012">tribolium2012</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
251 <option value="trichinella">Trichinella</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
252 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
253 <option value="Trypanosoma_cruzi">Trypanosoma cruzi</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
254 <option value="ustilago">Ustilago</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
255 <option value="ustilago_maydis">Ustilago maydis</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
256 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
257 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
258 <option value="Vitis_vinifera">Vitis vinifera</option>
7
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259 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option>
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260 <option value="volvox">volvox</option>
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261 <option value="wheat">wheat</option>
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262 <option value="Xenopus_tropicalis">Xenopus tropicalis</option>
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263 <option value="Xiphophorus_maculatus">Xiphophorus maculatus</option>
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264 <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
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265 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
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266 <option value="zebrafish">Danio rerio (zebrafish)</option>
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267 </param>
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268 </when>
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269 </conditional>
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270
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271 <param type="boolean" argument="--softmasking" label="Softmasking" truevalue="1" falsevalue="0" checked="true" help="If this option is enabled, lowercase letters are considered as repeated regions." />
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272 <param type="select" argument="--strand" label="Predict genes on specific strands">
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273 <option value="both">both</option>
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274 <option value="forward">forward</option>
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275 <option value="backward">backward</option>
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276 </param>
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277 <param argument="--genemodel" label="Gene Model" type="select"
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278 help="Gene Model to predict, for more information please refer to the help.">
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279 <option value="complete">complete</option>
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280 <option value="partial">partial</option>
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281 <option value="intronless">intronless</option>
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282 <option value="atleastone">atleastone</option>
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283 <option value="exactlyone">exactlyone</option>
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284 </param>
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285 <conditional name="hints">
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286 <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
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287 <option value="F">No</option>
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288 <option value="T">Yes</option>
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289 </param>
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290 <when value="T">
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291 <param argument="--hintsfile" label="Select hints file from history" type="data" format="gff"
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292 help="A file containing hints in gff format"/>
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293 <param name="extrinsiccfg" argument="--extrinsicCfgFile" label="Select extrinsic configuration file from history" type="data" format="txt"
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294 help="A .cfg file listing hint sources and their boni and mali"/>
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295 </when>
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296 <when value="F">
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297 </when>
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298 </conditional>
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299 <conditional name="range">
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300 <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
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301 <option value="F">No</option>
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302 <option value="T">Yes</option>
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303 </param>
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304 <when value="T">
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305 <param name="start" argument="--predictionStart" label="Starting position" type="integer" value=""
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306 help="The beginning of the search range"/>
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307 <param name="stop" argument="--predictionEnd" label="Ending position" type="integer" value=""
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308 help="The end of the search range; must be greater than starting position"/>
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309 </when>
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310 <when value="F">
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311 </when>
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312 </conditional>
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313 <param name="gff" argument="--gff3" type="boolean" label="GFF formated output" help="Standard output is GTF." truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
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314 <param name="outputs" type="select" optional="true" multiple="true" label="Output options">
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315 <option value="protein" selected="true">predicted protein sequences (--protein)</option>
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316 <option value="codingseq" selected="true">coding sequence as comment in the output file (--codingseq)</option>
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317 <option value="introns">predicted intron sequences (--introns)</option>
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318 <option value="start">predicted start codons (--start)</option>
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319 <option value="stop">predicted stop codons (--stop)</option>
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320 <option value="cds" selected="true">CDS region (--cds)</option>
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321 </param>
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322 </inputs>
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323 <outputs>
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324 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
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325 <change_format>
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326 <when input="gff" value="--gff3=on" format="gff3" />
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327 </change_format>
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328 </data>
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329 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
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330 <filter>outputs and 'protein' in outputs</filter>
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331 </data>
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332 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
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333 <filter>outputs and 'codingseq' in outputs</filter>
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334 </data>
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335 </outputs>
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336 <tests>
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337 <test expect_num_outputs="3">
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338 <param name="input_genome" value="human_augustus.fa.gz" ftype="fasta.gz" />
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339 <conditional name="model">
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340 <param name="organism" value="human" />
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341 </conditional>
3
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342 <param name="utr" value="True" />
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343 <param name="softmasking" value="False"/>
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344 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
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345 </test>
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346 <test expect_num_outputs="3">
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347 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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348 <conditional name="model">
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349 <param name="organism" value="human" />
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350 </conditional>
3
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351 <param name="utr" value="True" />
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352 <param name="gff" value="True" />
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353 <param name="softmasking" value="False"/>
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354 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
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355 </test>
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356 <test expect_num_outputs="3">
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357 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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358 <conditional name="model">
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359 <param name="organism" value="human" />
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360 </conditional>
3
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361 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
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362 <param name="softmasking" value="False"/>
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363 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
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364 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
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365 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
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366 </test>
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367 <test expect_num_outputs="1">
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368 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
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369 <conditional name="model">
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370 <param name="organism" value="fly" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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371 </conditional>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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parents: 10
diff changeset
372 <conditional name="hints">
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373 <param name="usehints" value="T" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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374 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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375 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
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376 </conditional>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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377 <param name="outputs" value_json="null" />
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378 <param name="softmasking" value="False"/>
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379 <param name="outputs" value=""/>
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380 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
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381 <assert_contents>
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382 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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383 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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384 </assert_contents>
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385 </output>
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386
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387 </test>
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388 <test expect_num_outputs="1">
5
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389 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
11
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parents: 10
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390 <conditional name="model">
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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parents: 10
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391 <param name="organism" value="fly" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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392 </conditional>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
diff changeset
393 <conditional name="hints">
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
parents: 10
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394 <param name="usehints" value="T" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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parents: 10
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395 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
iuc
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396 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
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397 </conditional>
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398 <conditional name="range">
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399 <param name="userange" value="T" />
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400 <param name="start" value="7000" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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401 <param name="stop" value="9000" />
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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402 </conditional>
534814b64234 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
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403 <param name="outputs" value_json="null" />
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404 <param name="softmasking" value="False"/>
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405 <param name="outputs" value_json="null"/>
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406 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
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407 <assert_contents>
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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408 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
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409 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
b3f5d0879dab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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410 </assert_contents>
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411 </output>
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412 </test>
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413 <!-- Test softmasking parameter-->
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414 <test expect_num_outputs="1">
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415 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
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416 <conditional name="model">
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417 <param name="organism" value="human" />
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418 </conditional>
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419 <param name="utr" value="True" />
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420 <param name="softmasking" value="True"/>
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421 <param name="outputs" value_json="null"/>
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422 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
09855551d713 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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423 </test>
5
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424
0
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425 </tests>
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426 <help>
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427 <![CDATA[
0
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428
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429 **What it does**
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430
4
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431 AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller.
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432 It can be used as an ab initio program, which means it bases its prediction purely on the
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433 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
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434 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
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435
4
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436
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437 **Input**
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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438
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439 Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence.
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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440
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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441
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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442 **Output**
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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443
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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444 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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445
0
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446
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447 **Parameters**
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448
4
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449 Gene Model:
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450
4
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451 partial: allow prediction of incomplete genes at the sequence boundaries (default)
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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452 intronless: only predict single-exon genes like in prokaryotes and some eukaryotes
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453 complete: only predict complete genes
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454 atleastone: predict at least one complete gene
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455 exactlyone: predict exactly one complete gene
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456
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457
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458
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459 **Example**
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460
4
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461 Suppose you have the following DNA FASTA sequence:
0
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462
4
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463 >Seq1
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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464 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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465 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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466 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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467 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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468 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
0
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469
4
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470
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471 Running this tool will produce this:
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472
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473 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
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474 #
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475 # Constraints/Hints:
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476 # (none)
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477 # Predicted genes for sequence number 1 on both strands
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478 # start gene g1
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479 scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
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480 scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
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481 scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
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482 scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
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483 scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
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484 scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
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485 scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
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486 scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
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487 scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
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488 scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
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489 scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
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490 scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
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491 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
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492 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
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493 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
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494
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495
2
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parents: 1
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496 ]]>
0
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497 </help>
4
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498 <expand macro="citations"/>
0
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499 </tool>