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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
author iuc
date Fri, 04 Oct 2024 11:32:08 +0000
parents 09855551d713
children
comparison
equal deleted inserted replaced
8:28433faa6e42 9:bd0e53f3a891
1 <tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@"> 1 <tool id="augustus" name="Augustus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>gene prediction for prokaryotic and eukaryotic genomes</description> 2 <description>gene prediction for prokaryotic and eukaryotic genomes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">augustus</xref>
8 </xrefs>
6 <expand macro="requirements"/> 9 <expand macro="requirements"/>
7 <command detect_errors="aggressive"> 10 <command detect_errors="aggressive">
8 <![CDATA[ 11 <![CDATA[
9 #if $model.augustus_mode == 'history' 12 #if $model.augustus_mode == 'history'
10 13
95 #end if 98 #end if
96 ]]> 99 ]]>
97 </command> 100 </command>
98 <inputs> 101 <inputs>
99 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> 102 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
100 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean" 103 <param argument="--noInFrameStop" type="boolean"
101 label="Don't report transcripts with in-frame stop codons" 104 label="Don't report transcripts with in-frame stop codons"
102 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" 105 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
103 help="Otherwise, intron-spanning stop codons could occur." /> 106 help="Otherwise, intron-spanning stop codons could occur." />
104 <param name="singlestrand" type="boolean" argument="--singlestrand" 107 <param type="boolean" argument="--singlestrand"
105 label="Predict genes independently on each strand" 108 label="Predict genes independently on each strand"
106 help="This allows overlapping genes on opposite strands." 109 help="This allows overlapping genes on opposite strands."
107 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> 110 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
108 111
109 <param name="utr" type="boolean" argument="--UTR" 112 <param name="utr" type="boolean" argument="--UTR"
116 <param name="augustus_mode" type="select" label="Trainingset"> 119 <param name="augustus_mode" type="select" label="Trainingset">
117 <option value="builtin">Run Augustus with a predefined trainingset</option> 120 <option value="builtin">Run Augustus with a predefined trainingset</option>
118 <option value="history">Run Augustus with a custom trainingset</option> 121 <option value="history">Run Augustus with a custom trainingset</option>
119 </param> 122 </param>
120 <when value="history"> 123 <when value="history">
121 <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/> 124 <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
122 </when> 125 </when>
123 <when value="builtin"> 126 <when value="builtin">
124 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> 127 <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
125 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) --> 128 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
126 <option value="human">Homo sapiens</option> 129 <option value="human">Homo sapiens</option>
127 <option value="fly">Drosophila melanogaster</option> 130 <option value="fly">Drosophila melanogaster</option>
128 <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option> 131 <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option>
129 <option value="arabidopsis">Arabidopsis thaliana</option> 132 <option value="arabidopsis">Arabidopsis thaliana</option>
130 <option value="brugia ">Brugia malayi</option> 133 <option value="brugia">Brugia malayi (brugia)</option>
134 <option value="brugia_malayi">Brugia malayi (brugia_malayi)</option>
131 <option value="aedes">Aedes aegypti</option> 135 <option value="aedes">Aedes aegypti</option>
132 <option value="tribolium2012">Tribolium castaneum</option> 136 <option value="tribolium2012">Tribolium castaneum</option>
133 <option value="schistosoma">Schistosoma mansoni</option> 137 <option value="schistosoma">Schistosoma mansoni</option>
134 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option> 138 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
135 <option value="tetrahymena">Tetrahymena thermophila</option> 139 <option value="tetrahymena">Tetrahymena thermophila</option>
136 <option value="galdieria">Galdieria sulphuraria</option> 140 <option value="galdieria">Galdieria sulphuraria</option>
137 <option value="maize">Zea mays</option> 141 <option value="maize">Zea mays</option>
138 <option value="toxoplasma">Toxoplasma gondii</option> 142 <option value="toxoplasma">Toxoplasma gondii</option>
139 <option value="caenorhabditis ">Caenorhabditis elegans</option> 143 <option value="caenorhabditis">Caenorhabditis elegans</option>
140 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> 144 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
141 <option value="aspergillus_nidulans ">Aspergillus nidulans</option> 145 <option value="anidulans">Aspergillus nidulans (anidulans)</option>
142 <option value="aspergillus_oryzae ">Aspergillus oryzae</option> 146 <option value="aspergillus_nidulans">Aspergillus nidulans (aspergillus_nidulans)</option>
147 <option value="aspergillus_oryzae">Aspergillus oryzae</option>
143 <option value="aspergillus_terreus">Aspergillus terreus</option> 148 <option value="aspergillus_terreus">Aspergillus terreus</option>
144 <option value="botrytis_cinerea ">Botrytis cinerea</option> 149 <option value="botrytis_cinerea">Botrytis cinerea</option>
145 <option value="candida_albicans ">Candida albicans</option> 150 <option value="candida_albicans">Candida albicans</option>
146 <option value="candida_guilliermondii ">Candida guilliermondii</option> 151 <option value="candida_guilliermondii">Candida guilliermondii</option>
147 <option value="candida_tropicalis ">Candida tropicalis</option> 152 <option value="candida_tropicalis">Candida tropicalis</option>
148 <option value="chaetomium_globosum">Chaetomium globosum</option> 153 <option value="chaetomium_globosum">Chaetomium globosum</option>
149 <option value="coccidioides_immitis">Coccidioides immitis</option> 154 <option value="coccidioides_immitis">Coccidioides immitis</option>
150 <option value="coprinus">Coprinus cinereus</option> 155 <option value="coprinus">Coprinus cinereus (coprinus)</option>
151 <option value="coprinus_cinereus">Coprinus cinereus</option> 156 <option value="coprinus_cinereus">Coprinus cinereus (coprinus_cinereus)</option>
152 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> 157 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
153 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> 158 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
154 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> 159 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
155 <option value="cryptococcus">Cryptococcus neoformans</option> 160 <option value="cryptococcus">Cryptococcus neoformans (cryptococcus)</option>
161 <option value="cryptococcus_neoformans">Cryptococcus neoformans (cryptococcus_neoformans)</option>
156 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> 162 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
157 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> 163 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
164 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
158 <option value="eremothecium_gossypii">Eremothecium gossypii</option> 165 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
159 <option value="fusarium_graminearum ">Fusarium graminearum</option> 166 <option value="fusarium_graminearum">Fusarium graminearum</option>
160 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> 167 <option value="histoplasma_capsulatum">Histoplasma capsulatum (histoplasma_capsulatum)</option>
161 <option value="histoplasma">Histoplasma capsulatum</option> 168 <option value="histoplasma">Histoplasma capsulatum (histoplasma)</option>
162 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> 169 <option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
163 <option value="laccaria_bicolor ">Laccaria bicolor</option> 170 <option value="laccaria_bicolor">Laccaria bicolor</option>
164 <option value="lamprey">Petromyzon marinus</option> 171 <option value="lamprey">Petromyzon marinus</option>
165 <option value="leishmania_tarentolae">Leishmania tarentolae</option> 172 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
166 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> 173 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
167 <option value="magnaporthe_grisea ">Magnaporthe grisea</option> 174 <option value="magnaporthe_grisea">Magnaporthe grisea</option>
168 <option value="neurospora_crassa">Neurospora crassa</option> 175 <option value="neurospora_crassa">Neurospora crassa</option>
169 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> 176 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
170 <option value="pichia_stipitis">Pichia stipitis</option> 177 <option value="pichia_stipitis">Pichia stipitis</option>
171 <option value="rhizopus_oryzae">Rhizopus oryzae</option> 178 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
172 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> 179 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae saccharomyces_cerevisiae_S288C</option>
173 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> 180 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae RM11-1a-1</option>
174 <option value="saccharomyces">Saccharomyces cerevisiae</option> 181 <option value="saccharomyces">Saccharomyces cerevisiae (saccharomyces)</option>
175 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> 182 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
176 <option value="trichinella">Trichinella spiralis</option> 183 <option value="trichinella">Trichinella spiralis</option>
177 <option value="ustilago_maydis">Ustilago maydis</option>
178 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> 184 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
179 <option value="nasonia">Nasonia vitripennis</option> 185 <option value="nasonia">Nasonia vitripennis</option>
180 <option value="tomato">Solanum lycopersicum</option> 186 <option value="tomato">Solanum lycopersicum</option>
181 <option value="chlamydomonas">Chlamydomonas reinhardtii</option> 187 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
182 <option value="amphimedon">Amphimedon queenslandica</option> 188 <option value="amphimedon">Amphimedon queenslandica</option>
191 <option value="coyote_tobacco">Coyote tobacco</option> 197 <option value="coyote_tobacco">Coyote tobacco</option>
192 <option value="s_aureus">Staphylococcus aureus</option> 198 <option value="s_aureus">Staphylococcus aureus</option>
193 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> 199 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
194 <option value="wheat">Triticum aestivum</option> 200 <option value="wheat">Triticum aestivum</option>
195 <option value="zebrafish">Danio rerio</option> 201 <option value="zebrafish">Danio rerio</option>
196 <option value="anidulans">Aspergillus nidulans</option>
197 <option value="bombus_impatiens1">Bombus impatiens1</option> 202 <option value="bombus_impatiens1">Bombus impatiens1</option>
198 <option value="bombus_terrestris2">Bombus terrestris2</option> 203 <option value="bombus_terrestris2">Bombus terrestris2</option>
199 <option value="botrytis_cinerea">Botrytis cinerea</option>
200 <option value="brugia_malayi">Brugia malayi</option>
201 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> 204 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
202 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
203 <option value="culex_pipiens">Culex pipiens</option> 205 <option value="culex_pipiens">Culex pipiens</option>
204 <option value="elephant_shark">Callorhinchus milii</option> 206 <option value="elephant_shark">Callorhinchus milii</option>
205 <option value="honeybee1">Apis mellifera</option> 207 <option value="honeybee1">Apis mellifera</option>
206 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
207 <option value="pea_aphid">Acyrthosiphon pisum</option> 208 <option value="pea_aphid">Acyrthosiphon pisum</option>
208 <option value="rhodnius_prolixus">Rhodnius prolixus</option> 209 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
209 <option value="ustilago_maydis">Ustilago maydis</option> 210 <option value="ustilago_maydis">Ustilago maydis</option>
210 <option value="verticillium_albo_atrum1">Verticillium albo-atrum</option> 211 <option value="verticillium_albo_atrum1">Verticillium albo-atrum</option>
211 <option value="verticillium_longisporum1">Verticillium longisporum</option> 212 <option value="verticillium_longisporum1">Verticillium longisporum</option>
225 <option value="Chrysaora_chesapeakeij">Chrysaora chesapeakeij</option> 226 <option value="Chrysaora_chesapeakeij">Chrysaora chesapeakeij</option>
226 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option> 227 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
227 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option> 228 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
228 <option value="Aurelia_aurita">Aurelia aurita</option> 229 <option value="Aurelia_aurita">Aurelia aurita</option>
229 <option value="Rhopilema_esculentum">Rhopilema esculentum</option> 230 <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
230 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
231 <option value="Gonapodya_prolifera">Dunaliella salina</option> 231 <option value="Gonapodya_prolifera">Dunaliella salina</option>
232 <option value="Sordaria_macrospora">Sordaria macrospora</option> 232 <option value="Sordaria_macrospora">Sordaria macrospora</option>
233 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option> 233 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
234 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option> 234 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option>
235 <option value="Monoraphidium_neglectum">Monoraphidium_neglectum</option> 235 <option value="Monoraphidium_neglectum">Monoraphidium_neglectum</option>
248 <option value="Chloropicon_primus">Chloropicon primus</option> 248 <option value="Chloropicon_primus">Chloropicon primus</option>
249 </param> 249 </param>
250 </when> 250 </when>
251 </conditional> 251 </conditional>
252 252
253 <param name="softmasking" type="boolean" argument="--softmasking" 253 <param type="boolean" argument="--softmasking"
254 label="Softmasking" 254 label="Softmasking"
255 truevalue="1" falsevalue="0" checked="true" 255 truevalue="1" falsevalue="0" checked="true"
256 help="If this option is enabled, lowercase letters are considered as repeated regions." /> 256 help="If this option is enabled, lowercase letters are considered as repeated regions." />
257 257
258 258
259 <param name="strand" type="select" argument="--strand" 259 <param type="select" argument="--strand"
260 label="Predict genes on specific strands"> 260 label="Predict genes on specific strands">
261 <option value="both">both</option> 261 <option value="both">both</option>
262 <option value="forward">forward</option> 262 <option value="forward">forward</option>
263 <option value="backward">backward</option> 263 <option value="backward">backward</option>
264 </param> 264 </param>
265 265
266 <param name="genemodel" label="Gene Model" type="select" 266 <param argument="--genemodel" label="Gene Model" type="select"
267 help="Gene Model to predict, for more information please refer to the help."> 267 help="Gene Model to predict, for more information please refer to the help.">
268 <option value="complete">complete</option> 268 <option value="complete">complete</option>
269 <option value="partial">partial</option> 269 <option value="partial">partial</option>
270 <option value="intronless">intronless</option> 270 <option value="intronless">intronless</option>
271 <option value="atleastone">atleastone</option> 271 <option value="atleastone">atleastone</option>
276 <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio"> 276 <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
277 <option value="F">No</option> 277 <option value="F">No</option>
278 <option value="T">Yes</option> 278 <option value="T">Yes</option>
279 </param> 279 </param>
280 <when value="T"> 280 <when value="T">
281 <param name="hintsfile" label="Select hints file from history" type="data" format="gff" 281 <param argument="--hintsfile" label="Select hints file from history" type="data" format="gff"
282 help="A file containing hints in gff format (--hintsfile)"/> 282 help="A file containing hints in gff format"/>
283 <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt" 283 <param name="extrinsiccfg" argument="--extrinsicCfgFile" label="Select extrinsic configuration file from history" type="data" format="txt"
284 help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/> 284 help="A .cfg file listing hint sources and their boni and mali"/>
285 </when> 285 </when>
286 <when value="F"> 286 <when value="F">
287 </when> 287 </when>
288 </conditional> 288 </conditional>
289 289
291 <param name="userange" label="Specify prediction sequence range?" type="select" display="radio"> 291 <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
292 <option value="F">No</option> 292 <option value="F">No</option>
293 <option value="T">Yes</option> 293 <option value="T">Yes</option>
294 </param> 294 </param>
295 <when value="T"> 295 <when value="T">
296 <param name="start" label="Starting position" type="integer" value="" 296 <param name="start" argument="--predictionStart" label="Starting position" type="integer" value=""
297 help="The beginning of the search range (--predictionStart)"/> 297 help="The beginning of the search range"/>
298 <param name="stop" label="Ending position" type="integer" value="" 298 <param name="stop" argument="--predictionEnd" label="Ending position" type="integer" value=""
299 help="The end of the search range (--predictionEnd); must be greater than starting position"/> 299 help="The end of the search range; must be greater than starting position"/>
300 </when> 300 </when>
301 <when value="F"> 301 <when value="F">
302 </when> 302 </when>
303 </conditional> 303 </conditional>
304 304
305 <param name="gff" type="boolean" label="GFF formated output" 305 <param name="gff" argument="--gff3" type="boolean" label="GFF formated output"
306 help="Standard output is GTF." 306 help="Standard output is GTF."
307 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> 307 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
308 308
309 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> 309 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
310 <option value="protein" selected="True">predicted protein sequences (--protein)</option> 310 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
327 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence"> 327 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
328 <filter>'codingseq' in outputs</filter> 328 <filter>'codingseq' in outputs</filter>
329 </data> 329 </data>
330 </outputs> 330 </outputs>
331 <tests> 331 <tests>
332 <test> 332 <test expect_num_outputs="3">
333 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 333 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
334 <param name="organism" value="human" /> 334 <param name="organism" value="human" />
335 <param name="utr" value="True" /> 335 <param name="utr" value="True" />
336 <param name="softmasking" value="False"/> 336 <param name="softmasking" value="False"/>
337 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/> 337 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
338 </test> 338 </test>
339 <test> 339 <test expect_num_outputs="3">
340 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 340 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
341 <param name="organism" value="human" /> 341 <param name="organism" value="human" />
342 <param name="utr" value="True" /> 342 <param name="utr" value="True" />
343 <param name="gff" value="True" /> 343 <param name="gff" value="True" />
344 <param name="softmasking" value="False"/> 344 <param name="softmasking" value="False"/>
345 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/> 345 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
346 </test> 346 </test>
347 <test> 347 <test expect_num_outputs="3">
348 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 348 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
349 <param name="organism" value="human" /> 349 <param name="organism" value="human" />
350 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" /> 350 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
351 <param name="softmasking" value="False"/> 351 <param name="softmasking" value="False"/>
352 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/> 352 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
353 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> 353 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
354 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> 354 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
355 </test> 355 </test>
356 <test> 356 <test expect_num_outputs="1">
357 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" /> 357 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
358 <param name="organism" value="fly" /> 358 <param name="organism" value="fly" />
359 <param name="usehints" value="T" /> 359 <param name="usehints" value="T" />
360 <param name="hintsfile" value="hints.truncated.adjusted.gff" /> 360 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
361 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> 361 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
362 <param name="outputs" value="" /> 362 <param name="outputs" value="" />
363 <param name="softmasking" value="False"/> 363 <param name="softmasking" value="False"/>
364 <param name="outputs" value=""/>
364 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12"> 365 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
365 <assert_contents> 366 <assert_contents>
366 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" /> 367 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
367 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" /> 368 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
368 </assert_contents> 369 </assert_contents>
369 </output> 370 </output>
370 371
371 </test> 372 </test>
372 <test> 373 <test expect_num_outputs="1">
373 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" /> 374 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
374 <param name="organism" value="fly" /> 375 <param name="organism" value="fly" />
375 <param name="usehints" value="T" /> 376 <param name="usehints" value="T" />
376 <param name="hintsfile" value="hints.truncated.adjusted.gff" /> 377 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
377 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> 378 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
378 <param name="userange" value="T" /> 379 <param name="userange" value="T" />
379 <param name="start" value="7000" /> 380 <param name="start" value="7000" />
380 <param name="stop" value="9000" /> 381 <param name="stop" value="9000" />
381 <param name="outputs" value="" /> 382 <param name="outputs" value="" />
382 <param name="softmasking" value="False"/> 383 <param name="softmasking" value="False"/>
384 <param name="outputs" value=""/>
383 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12"> 385 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
384 <assert_contents> 386 <assert_contents>
385 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" /> 387 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
386 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" /> 388 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
387 </assert_contents> 389 </assert_contents>
388 </output> 390 </output>
389 </test> 391 </test>
390 <!-- Test softmasking parameter--> 392 <!-- Test softmasking parameter-->
391 <test> 393 <test expect_num_outputs="1">
392 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 394 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
393 <param name="organism" value="human" /> 395 <param name="organism" value="human" />
394 <param name="utr" value="True" /> 396 <param name="utr" value="True" />
395 <param name="softmasking" value="True"/> 397 <param name="softmasking" value="True"/>
398 <param name="outputs" value=""/>
396 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/> 399 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
397 </test> 400 </test>
398 401
399 </tests> 402 </tests>
400 <help> 403 <help>