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comparison augustus.xml @ 4:4de31938431b draft

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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
parents f5075dee9d6b
children b3f5d0879dab
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3:f5075dee9d6b 4:4de31938431b
1 <tool id="augustus" name="Augustus" version="3.1.0"> 1 <tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@">
2 <description>gene prediction for eukaryotic genomes</description> 2 <description>gene prediction for prokaryotic and eukaryotic genomes</description>
3 <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism> 3 <macros>
4 <requirements> 4 <import>macros.xml</import>
5 <requirement type="package" version="3.1">augustus</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements"/>
7 <stdio> 7 <command detect_errors="aggressive">
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <regex match="Error:" />
11 <regex match="Exception:" />
12 </stdio>
13 <command>
14 <![CDATA[ 8 <![CDATA[
9 #if $model.augustus_mode == 'history'
10
11 ## Using an augustus model from history, we need to unzip it and let augustus find it
12
13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
14
15 mkdir -p 'augustus_dir/species/' &&
16
17 tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null &&
18
19 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
20 #end if
21
15 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external 22 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
16 ## script is used to extract the sequences into additional files 23 ## script is used to extract the sequences into additional files
17 24
18 augustus 25 augustus
19 --strand=$strand 26 --strand=$strand
59 66
60 $singlestrand 67 $singlestrand
61 $input_genome 68 $input_genome
62 $utr 69 $utr
63 --genemodel=$genemodel 70 --genemodel=$genemodel
64 --species=$organism 71
65 72
66 | tee $output 73 #if $model.augustus_mode == 'history'
74 --species=local
75 #else
76 --species=$model.organism
77 #end if
78
79 | tee '$output'
67 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','): 80 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
68 | python $__tool_directory__/extract_features.py 81 | python $__tool_directory__/extract_features.py
69 #if 'protein' in str($outputs).split(','): 82 #if 'protein' in str($outputs).split(','):
70 --protein $protein_output 83 --protein $protein_output
71 #end if 84 #end if
76 ]]> 89 ]]>
77 </command> 90 </command>
78 <inputs> 91 <inputs>
79 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> 92 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
80 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean" 93 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"
81 label="Don't report transcripts with in-frame stop codons (--noInFrameStop)" 94 label="Don't report transcripts with in-frame stop codons"
82 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" 95 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
83 help="Otherwise, intron-spanning stop codons could occur. (--noInFrameStop)" /> 96 help="Otherwise, intron-spanning stop codons could occur." />
84 <param name="singlestrand" type="boolean" argument="--singlestrand" 97 <param name="singlestrand" type="boolean" argument="--singlestrand"
85 label="Predict genes independently on each strand" 98 label="Predict genes independently on each strand"
86 help="This allows overlapping genes on opposite strands. (--singlestrand)" 99 help="This allows overlapping genes on opposite strands."
87 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> 100 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
88 101
89 <param name="utr" type="boolean" argument="--UTR" 102 <param name="utr" type="boolean" argument="--UTR"
90 label="Predict the untranslated regions in addition to the coding sequence" 103 label="Predict the untranslated regions in addition to the coding sequence"
91 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" 104 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
92 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis. (--UTR)" /> 105 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
93 106
94 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> 107
95 <option value="human">Homo sapiens</option> 108 <conditional name="model">
96 <option value="fly">Drosophila melanogaster</option> 109 <param name="augustus_mode" type="select" label="Trainingset">
97 <option value="arabidopsis">Arabidopsis thaliana</option> 110 <option value="builtin">Run Augustus with a predefined trainingset</option>
98 <option value="brugia ">Brugia malayi</option> 111 <option value="history">Run Augustus with a custom trainingset</option>
99 <option value="aedes">Aedes aegypti</option> 112 </param>
100 <option value="tribolium2012">Tribolium castaneum</option> 113 <when value="history">
101 <option value="schistosoma">Schistosoma mansoni</option> 114 <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
102 <option value="tetrahymena">Tetrahymena thermophila</option> 115 </when>
103 <option value="galdieria">Galdieria sulphuraria</option> 116 <when value="builtin">
104 <option value="maize">Zea mays</option> 117 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
105 <option value="toxoplasma">Toxoplasma gondii</option> 118 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
106 <option value="caenorhabditis ">Caenorhabditis elegans</option> 119 <option value="human">Homo sapiens</option>
107 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> 120 <option value="fly">Drosophila melanogaster</option>
108 <option value="aspergillus_nidulans ">Aspergillus nidulans</option> 121 <option value="arabidopsis">Arabidopsis thaliana</option>
109 <option value="aspergillus_oryzae ">Aspergillus oryzae</option> 122 <option value="brugia ">Brugia malayi</option>
110 <option value="aspergillus_terreus">Aspergillus terreus</option> 123 <option value="aedes">Aedes aegypti</option>
111 <option value="botrytis_cinerea ">Botrytis cinerea</option> 124 <option value="tribolium2012">Tribolium castaneum</option>
112 <option value="candida_albicans ">Candida albicans</option> 125 <option value="schistosoma">Schistosoma mansoni</option>
113 <option value="candida_guilliermondii ">Candida guilliermondii</option> 126 <option value="tetrahymena">Tetrahymena thermophila</option>
114 <option value="candida_tropicalis ">Candida tropicalis</option> 127 <option value="galdieria">Galdieria sulphuraria</option>
115 <option value="chaetomium_globosum">Chaetomium globosum</option> 128 <option value="maize">Zea mays</option>
116 <option value="coccidioides_immitis">Coccidioides immitis</option> 129 <option value="toxoplasma">Toxoplasma gondii</option>
117 <option value="coprinus">Coprinus cinereus</option> 130 <option value="caenorhabditis ">Caenorhabditis elegans</option>
118 <option value="coprinus_cinereus">Coprinus cinereus</option> 131 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
119 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> 132 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
120 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> 133 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
121 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> 134 <option value="aspergillus_terreus">Aspergillus terreus</option>
122 <option value="cryptococcus">Cryptococcus neoformans</option> 135 <option value="botrytis_cinerea ">Botrytis cinerea</option>
123 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> 136 <option value="candida_albicans ">Candida albicans</option>
124 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> 137 <option value="candida_guilliermondii ">Candida guilliermondii</option>
125 <option value="eremothecium_gossypii">Eremothecium gossypii</option> 138 <option value="candida_tropicalis ">Candida tropicalis</option>
126 <option value="fusarium_graminearum ">Fusarium graminearum</option> 139 <option value="chaetomium_globosum">Chaetomium globosum</option>
127 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> 140 <option value="coccidioides_immitis">Coccidioides immitis</option>
128 <option value="histoplasma">Histoplasma capsulatum</option> 141 <option value="coprinus">Coprinus cinereus</option>
129 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> 142 <option value="coprinus_cinereus">Coprinus cinereus</option>
130 <option value="laccaria_bicolor ">Laccaria bicolor</option> 143 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
131 <option value="lamprey">Petromyzon marinus</option> 144 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
132 <option value="leishmania_tarentolae">Leishmania tarentolae</option> 145 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
133 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> 146 <option value="cryptococcus">Cryptococcus neoformans</option>
134 <option value="magnaporthe_grisea ">Magnaporthe grisea</option> 147 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
135 <option value="neurospora_crassa">Neurospora crassa</option> 148 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
136 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> 149 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
137 <option value="pichia_stipitis">Pichia stipitis</option> 150 <option value="fusarium_graminearum ">Fusarium graminearum</option>
138 <option value="rhizopus_oryzae">Rhizopus oryzae</option> 151 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
139 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> 152 <option value="histoplasma">Histoplasma capsulatum</option>
140 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> 153 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
141 <option value="saccharomyces">Saccharomyces cerevisiae</option> 154 <option value="laccaria_bicolor ">Laccaria bicolor</option>
142 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> 155 <option value="lamprey">Petromyzon marinus</option>
143 <option value="trichinella">Trichinella spiralis</option> 156 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
144 <option value="ustilago_maydis">Ustilago maydis</option> 157 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
145 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> 158 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
146 <option value="nasonia">Nasonia vitripennis</option> 159 <option value="neurospora_crassa">Neurospora crassa</option>
147 <option value="tomato">Solanum lycopersicum</option> 160 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
148 <option value="chlamydomonas">Chlamydomonas reinhardtii</option> 161 <option value="pichia_stipitis">Pichia stipitis</option>
149 <option value="amphimedon">Amphimedon queenslandica</option> 162 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
150 <option value="pneumocystis">Pneumocystis jirovecii</option> 163 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
151 <option value="chicken">Gallus gallus domesticus (chicken)</option> 164 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
152 <option value="cacao">Theobroma cacao (cacao)</option> 165 <option value="saccharomyces">Saccharomyces cerevisiae</option>
153 <option value="heliconius_melpomene1">Heliconius melpomene</option> 166 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
154 <option value="xenoturbella">Xenoturbella</option> 167 <option value="trichinella">Trichinella spiralis</option>
155 <option value="E_coli_K12">E coli K12</option> 168 <option value="ustilago_maydis">Ustilago maydis</option>
156 <option value="c_elegans_trsk">c elegans trsk</option> 169 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
157 <option value="camponotus_floridanus">Camponotus floridanus</option> 170 <option value="nasonia">Nasonia vitripennis</option>
158 <option value="coyote_tobacco">Coyote tobacco</option> 171 <option value="tomato">Solanum lycopersicum</option>
159 <option value="s_aureus">Staphylococcus aureus</option> 172 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
160 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> 173 <option value="amphimedon">Amphimedon queenslandica</option>
161 <option value="wheat">wheat</option> 174 <option value="pneumocystis">Pneumocystis jirovecii</option>
162 <option value="zebrafish">Danio rerio</option> 175 <option value="chicken">Gallus gallus domesticus (chicken)</option>
163 <option value="anidulans">Aspergillus nidulans</option> 176 <option value="cacao">Theobroma cacao (cacao)</option>
164 <option value="bombus_impatiens1">Bombus impatiens1</option> 177 <option value="heliconius_melpomene1">Heliconius melpomene</option>
165 <option value="bombus_terrestris2">Bombus terrestris2</option> 178 <option value="xenoturbella">Xenoturbella</option>
166 <option value="botrytis_cinerea">Botrytis cinerea</option> 179 <option value="E_coli_K12">E coli K12</option>
167 <option value="brugia_malayi">Brugia malayi</option> 180 <option value="c_elegans_trsk">c elegans trsk</option>
168 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> 181 <option value="camponotus_floridanus">Camponotus floridanus</option>
169 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option> 182 <option value="coyote_tobacco">Coyote tobacco</option>
170 <option value="culex_pipiens">Culex pipiens</option> 183 <option value="s_aureus">Staphylococcus aureus</option>
171 <option value="elephant_shark">Callorhinchus milii</option> 184 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
172 <option value="honeybee1">Apis mellifera</option> 185 <option value="wheat">wheat</option>
173 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> 186 <option value="zebrafish">Danio rerio</option>
174 <option value="pea_aphid">Acyrthosiphon pisum</option> 187 <option value="anidulans">Aspergillus nidulans</option>
175 <option value="rhodnius_prolixus">Rhodnius prolixus</option> 188 <option value="bombus_impatiens1">Bombus impatiens1</option>
176 <option value="ustilago_maydis">Ustilago maydis</option> 189 <option value="bombus_terrestris2">Bombus terrestris2</option>
177 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> 190 <option value="botrytis_cinerea">Botrytis cinerea</option>
178 <option value="verticillium_longisporum1">Verticillium longisporum1</option> 191 <option value="brugia_malayi">Brugia malayi</option>
179 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> 192 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
180 <option value="adorsata">adorsata</option> 193 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
181 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> 194 <option value="culex_pipiens">Culex pipiens</option>
182 <option value="maker2_athal1">maker2_athal1</option> 195 <option value="elephant_shark">Callorhinchus milii</option>
183 <option value="maker2_c_elegans1">maker2_c_elegans1</option> 196 <option value="honeybee1">Apis mellifera</option>
184 <option value="maker2_dmel1">maker2_dmel1</option> 197 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
185 <option value="maker2_spomb1">maker2_spomb1</option> 198 <option value="pea_aphid">Acyrthosiphon pisum</option>
186 <option value="parasteatoda">parasteatoda</option> 199 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
187 <option value="rice">rice</option> 200 <option value="ustilago_maydis">Ustilago maydis</option>
188 <option value="schistosoma2">schistosoma2</option> 201 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
189 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> 202 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
190 </param> 203 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
204 <option value="adorsata">adorsata</option>
205 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
206 <option value="maker2_athal1">maker2_athal1</option>
207 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
208 <option value="maker2_dmel1">maker2_dmel1</option>
209 <option value="maker2_spomb1">maker2_spomb1</option>
210 <option value="parasteatoda">parasteatoda</option>
211 <option value="rice">rice</option>
212 <option value="schistosoma2">schistosoma2</option>
213 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
214 </param>
215 </when>
216 </conditional>
191 217
192 <param name="strand" type="select" argument="--strand" 218 <param name="strand" type="select" argument="--strand"
193 label="Predict genes on specific strands" help="(--strand)"> 219 label="Predict genes on specific strands">
194 <option value="both">both</option> 220 <option value="both">both</option>
195 <option value="forward">forward</option> 221 <option value="forward">forward</option>
196 <option value="backward">backward</option> 222 <option value="backward">backward</option>
197 </param> 223 </param>
198 224
199 <param name="genemodel" label="Gene Model" type="select" 225 <param name="genemodel" label="Gene Model" type="select"
200 help="Gene Model to predict, for more information please refere to the help. (--genemodel)"> 226 help="Gene Model to predict, for more information please refere to the help.">
201 <option value="complete">complete</option> 227 <option value="complete">complete</option>
202 <option value="partial">partial</option> 228 <option value="partial">partial</option>
203 <option value="intronless">intronless</option> 229 <option value="intronless">intronless</option>
204 <option value="atleastone">atleastone</option> 230 <option value="atleastone">atleastone</option>
205 <option value="exactlyone">exactlyone</option> 231 <option value="exactlyone">exactlyone</option>
206 </param> 232 </param>
207 233
208 <param name="gff" type="boolean" label="GFF formated output" 234 <param name="gff" type="boolean" label="GFF formated output"
209 help="Standard output is GTF. (--gff3)" 235 help="Standard output is GTF."
210 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> 236 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
211 237
212 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> 238 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
213 <option value="protein" selected="True">predicted protein sequences (--protein)</option> 239 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
214 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option> 240 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
215 <option value="introns">predicted intron sequences (--introns)</option> 241 <option value="introns">predicted intron sequences (--introns)</option>
216 <option value="start">predicted start codons (--start)</option> 242 <option value="start">predicted start codons (--start)</option>
217 <option value="stop">predicted stop codons (--stop)</option> 243 <option value="stop">predicted stop codons (--stop)</option>
218 <option value="cds" selected="true">CDS region (--cds)</option> 244 <option value="cds" selected="true">CDS region (--cds)</option>
219
220 <validator type="no_options" message="Please select at least one output file." />
221 </param> 245 </param>
222
223 </inputs> 246 </inputs>
224 <outputs> 247 <outputs>
225 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF"> 248 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
226 <change_format> 249 <change_format>
227 <when input="gff" value="--gff3=on" format="gff3" /> 250 <when input="gff" value="--gff3=on" format="gff3" />
260 <help> 283 <help>
261 <![CDATA[ 284 <![CDATA[
262 285
263 **What it does** 286 **What it does**
264 287
265 AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. 288 AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller.
266 It can be used as an ab initio program, which means it bases its prediction purely on the 289 It can be used as an ab initio program, which means it bases its prediction purely on the
267 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources 290 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
268 such as EST, MS/MS, protein alignments and synthenic genomic alignments. 291 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
269 292
270 ----- 293
294 **Input**
295
296 Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence.
297
298
299 **Output**
300
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.
302
271 303
272 **Parameters** 304 **Parameters**
273 305
274 Gene Model:: 306 Gene Model:
275 307
276 partial : allow prediction of incomplete genes at the sequence boundaries (default) 308 partial: allow prediction of incomplete genes at the sequence boundaries (default)
277 intronless : only predict single-exon genes like in prokaryotes and some eukaryotes 309 intronless: only predict single-exon genes like in prokaryotes and some eukaryotes
278 complete : only predict complete genes 310 complete: only predict complete genes
279 atleastone : predict at least one complete gene 311 atleastone: predict at least one complete gene
280 exactlyone : predict exactly one complete gene 312 exactlyone: predict exactly one complete gene
281 313
282 314
283 315
284 **Example** 316 **Example**
285 317
286 Suppose you have the following DNA formatted sequences:: 318 Suppose you have the following DNA FASTA sequence:
287 319
288 >Seq1 320 >Seq1
289 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg 321 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
290 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag 322 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
291 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc 323 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
292 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc 324 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
293 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg 325 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
294 326
295 Running this tool will produce this:: 327
328 Running this tool will produce this:
296 329
297 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- 330 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
298 # 331 #
299 # Constraints/Hints: 332 # Constraints/Hints:
300 # (none) 333 # (none)
317 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; 350 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
318 351
319 352
320 ]]> 353 ]]>
321 </help> 354 </help>
322 <citations> 355 <expand macro="citations"/>
323 <citation type="doi">10.1093/bioinformatics/btg1080</citation>
324 </citations>
325 </tool> 356 </tool>