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comparison augustus.xml @ 7:09855551d713 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
author iuc
date Thu, 15 Jul 2021 17:16:12 +0000
parents ca6d970d931c
children bd0e53f3a891
comparison
equal deleted inserted replaced
6:ca6d970d931c 7:09855551d713
1 <tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@"> 1 <tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@">
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 <expand macro="requirements"/> 6 <expand macro="requirements"/>
66 66
67 $singlestrand 67 $singlestrand
68 $input_genome 68 $input_genome
69 $utr 69 $utr
70 --genemodel=$genemodel 70 --genemodel=$genemodel
71 71 --softmasking=$softmasking
72 #if $hints.usehints == 'T' 72 #if $hints.usehints == 'T'
73 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg' 73 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
74 #end if 74 #end if
75 75
76 #if $range.userange == 'T' 76 #if $range.userange == 'T'
123 <when value="builtin"> 123 <when value="builtin">
124 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> 124 <param name="organism" 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) --> 125 <!-- 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> 126 <option value="human">Homo sapiens</option>
127 <option value="fly">Drosophila melanogaster</option> 127 <option value="fly">Drosophila melanogaster</option>
128 <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option>
128 <option value="arabidopsis">Arabidopsis thaliana</option> 129 <option value="arabidopsis">Arabidopsis thaliana</option>
129 <option value="brugia ">Brugia malayi</option> 130 <option value="brugia ">Brugia malayi</option>
130 <option value="aedes">Aedes aegypti</option> 131 <option value="aedes">Aedes aegypti</option>
131 <option value="tribolium2012">Tribolium castaneum</option> 132 <option value="tribolium2012">Tribolium castaneum</option>
132 <option value="schistosoma">Schistosoma mansoni</option> 133 <option value="schistosoma">Schistosoma mansoni</option>
134 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
133 <option value="tetrahymena">Tetrahymena thermophila</option> 135 <option value="tetrahymena">Tetrahymena thermophila</option>
134 <option value="galdieria">Galdieria sulphuraria</option> 136 <option value="galdieria">Galdieria sulphuraria</option>
135 <option value="maize">Zea mays</option> 137 <option value="maize">Zea mays</option>
136 <option value="toxoplasma">Toxoplasma gondii</option> 138 <option value="toxoplasma">Toxoplasma gondii</option>
137 <option value="caenorhabditis ">Caenorhabditis elegans</option> 139 <option value="caenorhabditis ">Caenorhabditis elegans</option>
181 <option value="pneumocystis">Pneumocystis jirovecii</option> 183 <option value="pneumocystis">Pneumocystis jirovecii</option>
182 <option value="chicken">Gallus gallus domesticus (chicken)</option> 184 <option value="chicken">Gallus gallus domesticus (chicken)</option>
183 <option value="cacao">Theobroma cacao (cacao)</option> 185 <option value="cacao">Theobroma cacao (cacao)</option>
184 <option value="heliconius_melpomene1">Heliconius melpomene</option> 186 <option value="heliconius_melpomene1">Heliconius melpomene</option>
185 <option value="xenoturbella">Xenoturbella</option> 187 <option value="xenoturbella">Xenoturbella</option>
186 <option value="E_coli_K12">E coli K12</option> 188 <option value="E_coli_K12">Escherichia coli K12</option>
187 <option value="c_elegans_trsk">c elegans trsk</option> 189 <option value="c_elegans_trsk">c elegans trsk</option>
188 <option value="camponotus_floridanus">Camponotus floridanus</option> 190 <option value="camponotus_floridanus">Camponotus floridanus</option>
189 <option value="coyote_tobacco">Coyote tobacco</option> 191 <option value="coyote_tobacco">Coyote tobacco</option>
190 <option value="s_aureus">Staphylococcus aureus</option> 192 <option value="s_aureus">Staphylococcus aureus</option>
191 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> 193 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
192 <option value="wheat">wheat</option> 194 <option value="wheat">Triticum aestivum</option>
193 <option value="zebrafish">Danio rerio</option> 195 <option value="zebrafish">Danio rerio</option>
194 <option value="anidulans">Aspergillus nidulans</option> 196 <option value="anidulans">Aspergillus nidulans</option>
195 <option value="bombus_impatiens1">Bombus impatiens1</option> 197 <option value="bombus_impatiens1">Bombus impatiens1</option>
196 <option value="bombus_terrestris2">Bombus terrestris2</option> 198 <option value="bombus_terrestris2">Bombus terrestris2</option>
197 <option value="botrytis_cinerea">Botrytis cinerea</option> 199 <option value="botrytis_cinerea">Botrytis cinerea</option>
203 <option value="honeybee1">Apis mellifera</option> 205 <option value="honeybee1">Apis mellifera</option>
204 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> 206 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
205 <option value="pea_aphid">Acyrthosiphon pisum</option> 207 <option value="pea_aphid">Acyrthosiphon pisum</option>
206 <option value="rhodnius_prolixus">Rhodnius prolixus</option> 208 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
207 <option value="ustilago_maydis">Ustilago maydis</option> 209 <option value="ustilago_maydis">Ustilago maydis</option>
208 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> 210 <option value="verticillium_albo_atrum1">Verticillium albo-atrum</option>
209 <option value="verticillium_longisporum1">Verticillium longisporum1</option> 211 <option value="verticillium_longisporum1">Verticillium longisporum</option>
210 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> 212 <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
211 <option value="adorsata">adorsata</option> 213 <option value="adorsata">Apis dorsata</option>
212 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> 214 <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
213 <option value="maker2_athal1">maker2_athal1</option> 215 <option value="maker2_athal1">Arabidopsis thaliana (maker2_athal1)</option>
214 <option value="maker2_c_elegans1">maker2_c_elegans1</option> 216 <option value="maker2_c_elegans1">Caenorhabditis elegans (maker2_c_elegans1)</option>
215 <option value="maker2_dmel1">maker2_dmel1</option> 217 <option value="maker2_spomb1">Saccharomyces cerevisiae (maker2_spomb1)</option>
216 <option value="maker2_spomb1">maker2_spomb1</option> 218 <option value="parasteatoda">Parasteatoda SP.</option>
217 <option value="parasteatoda">parasteatoda</option> 219 <option value="rice">Oryza sp.</option>
218 <option value="rice">rice</option> 220 <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
219 <option value="schistosoma2">schistosoma2</option> 221 <option value="Ptychodera_flava">Ptychodera flava</option>
220 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> 222 <option value="Argopecten_irridians">Argopecten irridians</option>
223 <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
224 <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
225 <option value="Chrysaora_chesapeakeij">Chrysaora chesapeakeij</option>
226 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
227 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
228 <option value="Aurelia_aurita">Aurelia aurita</option>
229 <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
230 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
231 <option value="Gonapodya_prolifera">Dunaliella salina</option>
232 <option value="Sordaria_macrospora">Sordaria macrospora</option>
233 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
234 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option>
235 <option value="Monoraphidium_neglectum">Monoraphidium_neglectum</option>
236 <option value="Raphidocelis_subcapita">Raphidocelis subcapita</option>
237 <option value="Ostreococcus_tauri">Ostreococcus tauri</option>
238 <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp. lucimarinus</option>
239 <option value="Micromonas_pusilla">Micromonas pusilla</option>
240 <option value="Micromonas_commoda">Micromonas commoda</option>
241 <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option>
242 <option value="Thalassiosira_pseudonana">Thalassiosira pseudonana</option>
243 <option value="Pseudo-nitzschia_multistriata">Pseudo-nitzschia multistriata</option>
244 <option value="Phaeodactylum_tricornutum">Phaeodactylum tricornutum</option>
245 <option value="Fragilariopsis_cylindrus">Fragilariopsis cylindrus</option>
246 <option value="Fistulifera_solaris">Fistulifera solaris</option>
247 <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
248 <option value="Chloropicon_primus">Chloropicon primus</option>
221 </param> 249 </param>
222 </when> 250 </when>
223 </conditional> 251 </conditional>
252
253 <param name="softmasking" type="boolean" argument="--softmasking"
254 label="Softmasking"
255 truevalue="1" falsevalue="0" checked="true"
256 help="If this option is enabled, lowercase letters are considered as repeated regions." />
257
224 258
225 <param name="strand" type="select" argument="--strand" 259 <param name="strand" type="select" argument="--strand"
226 label="Predict genes on specific strands"> 260 label="Predict genes on specific strands">
227 <option value="both">both</option> 261 <option value="both">both</option>
228 <option value="forward">forward</option> 262 <option value="forward">forward</option>
297 <tests> 331 <tests>
298 <test> 332 <test>
299 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 333 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
300 <param name="organism" value="human" /> 334 <param name="organism" value="human" />
301 <param name="utr" value="True" /> 335 <param name="utr" value="True" />
336 <param name="softmasking" value="False"/>
302 <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"/>
303 </test> 338 </test>
304 <test> 339 <test>
305 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 340 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
306 <param name="organism" value="human" /> 341 <param name="organism" value="human" />
307 <param name="utr" value="True" /> 342 <param name="utr" value="True" />
308 <param name="gff" value="True" /> 343 <param name="gff" value="True" />
344 <param name="softmasking" value="False"/>
309 <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"/>
310 </test> 346 </test>
311 <test> 347 <test>
312 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 348 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
313 <param name="organism" value="human" /> 349 <param name="organism" value="human" />
314 <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"/>
315 <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"/>
316 <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" />
317 <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" />
318 </test> 355 </test>
319 <test> 356 <test>
321 <param name="organism" value="fly" /> 358 <param name="organism" value="fly" />
322 <param name="usehints" value="T" /> 359 <param name="usehints" value="T" />
323 <param name="hintsfile" value="hints.truncated.adjusted.gff" /> 360 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
324 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> 361 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
325 <param name="outputs" value="" /> 362 <param name="outputs" value="" />
363 <param name="softmasking" value="False"/>
326 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12"> 364 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
327 <assert_contents> 365 <assert_contents>
328 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" /> 366 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
329 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" /> 367 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
330 </assert_contents> 368 </assert_contents>
339 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> 377 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
340 <param name="userange" value="T" /> 378 <param name="userange" value="T" />
341 <param name="start" value="7000" /> 379 <param name="start" value="7000" />
342 <param name="stop" value="9000" /> 380 <param name="stop" value="9000" />
343 <param name="outputs" value="" /> 381 <param name="outputs" value="" />
382 <param name="softmasking" value="False"/>
344 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12"> 383 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
345 <assert_contents> 384 <assert_contents>
346 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" /> 385 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
347 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" /> 386 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
348 </assert_contents> 387 </assert_contents>
349 </output> 388 </output>
389 </test>
390 <!-- Test softmasking parameter-->
391 <test>
392 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
393 <param name="organism" value="human" />
394 <param name="utr" value="True" />
395 <param name="softmasking" value="True"/>
396 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
350 </test> 397 </test>
351 398
352 </tests> 399 </tests>
353 <help> 400 <help>
354 <![CDATA[ 401 <![CDATA[