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comparison augustus.xml @ 11:534814b64234 draft default tip

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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
comparison
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10:0fc0f9cf035a 11:534814b64234
11 <![CDATA[ 11 <![CDATA[
12 #if $model.augustus_mode == 'history' 12 #if $model.augustus_mode == 'history'
13 13
14 ## Using an augustus model from history, we need to unzip it and let augustus find it 14 ## Using an augustus model from history, we need to unzip it and let augustus find it
15 15
16 cp -r `command -v augustus | xargs dirname`/../config/ augustus_dir/ && 16 cp -r \$(dirname \$(command -v augustus))/../config/ augustus_dir/ &&
17 17
18 mkdir -p 'augustus_dir/species/' && 18 mkdir -p 'augustus_dir/species/' &&
19 19
20 tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null && 20 tar -C 'augustus_dir/species/' -xzvf '$model.custom_model' > /dev/null &&
21 21
22 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 22 export AUGUSTUS_CONFIG_PATH=./augustus_dir/ &&
23 #end if 23 #end if
24 24
25 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external 25 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
26 ## script is used to extract the sequences into additional files 26 ## script is used to extract the sequences into additional files
27 27
29 --strand=$strand 29 --strand=$strand
30 $noInFrameStop 30 $noInFrameStop
31 $gff 31 $gff
32 --uniqueGeneId=true 32 --uniqueGeneId=true
33 33
34 #if 'protein' in str($outputs).split(','): 34 #for arg in ['protein', 'codingseq', 'introns', 'start', 'stop', 'cds']
35 --protein=on 35 #if arg in $outputs:
36 #else: 36 --$arg=on
37 --protein=off 37 #else
38 #end if 38 --$arg=off
39 39 #end if
40 #if 'codingseq' in str($outputs).split(','): 40 #end for
41 --codingseq=on
42 #else:
43 --codingseq=off
44 #end if
45
46 #if 'introns' in str($outputs).split(','):
47 --introns=on
48 #else:
49 --introns=off
50 #end if
51
52 #if 'start' in str($outputs).split(','):
53 --start=on
54 #else:
55 --stop=off
56 #end if
57
58 #if 'stop' in str($outputs).split(','):
59 --stop=on
60 #else:
61 --stop=off
62 #end if
63
64 #if 'cds' in str($outputs).split(','):
65 --cds=on
66 #else:
67 --cds=off
68 #end if
69
70 $singlestrand 41 $singlestrand
71 $input_genome 42 '$input_genome'
72 $utr 43 $utr
73 --genemodel=$genemodel 44 --genemodel=$genemodel
74 --softmasking=$softmasking 45 --softmasking=$softmasking
75 #if $hints.usehints == 'T' 46 #if $hints.usehints == 'T'
76 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg' 47 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
97 #end if 68 #end if
98 #end if 69 #end if
99 ]]> 70 ]]>
100 </command> 71 </command>
101 <inputs> 72 <inputs>
102 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> 73 <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genome Sequence"/>
103 <param argument="--noInFrameStop" type="boolean" 74 <param argument="--noInFrameStop" type="boolean"
104 label="Don't report transcripts with in-frame stop codons" 75 label="Don't report transcripts with in-frame stop codons"
105 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" 76 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
106 help="Otherwise, intron-spanning stop codons could occur." /> 77 help="Otherwise, intron-spanning stop codons could occur." />
107 <param type="boolean" argument="--singlestrand" 78 <param type="boolean" argument="--singlestrand"
122 </param> 93 </param>
123 <when value="history"> 94 <when value="history">
124 <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/> 95 <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
125 </when> 96 </when>
126 <when value="builtin"> 97 <when value="builtin">
127 <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="txt" help="Choose a specialised trainingset."> 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." >
128 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) --> 99 <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
129 <option value="human">Homo sapiens</option> 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 -->
130 <option value="fly">Drosophila melanogaster</option> 101 <option value="adorsata">Apis dorsata (adorsata)</option>
131 <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option> 102 <option value="aedes">Aedes aegypti (aedes)</option>
132 <option value="arabidopsis">Arabidopsis thaliana</option> 103 <option value="amphimedon">Amphimedon queenslandica</option>
133 <option value="brugia">Brugia malayi (brugia)</option> 104 <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
134 <option value="brugia_malayi">Brugia malayi (brugia_malayi)</option> 105 <option value="anidulans">Aspergillus nidulans (anidulans)</option>
135 <option value="aedes">Aedes aegypti</option> 106 <option value="Anopheles_gambiae">Anopheles gambiae</option>
136 <option value="tribolium2012">Tribolium castaneum</option> 107 <option value="arabidopsis">Arabidopsis thaliana (arabidopsis)</option>
137 <option value="schistosoma">Schistosoma mansoni</option> 108 <option value="Argopecten_irradians">Argopecten irradians</option>
138 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
139 <option value="tetrahymena">Tetrahymena thermophila</option>
140 <option value="galdieria">Galdieria sulphuraria</option>
141 <option value="maize">Zea mays</option>
142 <option value="toxoplasma">Toxoplasma gondii</option>
143 <option value="caenorhabditis">Caenorhabditis elegans</option>
144 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> 109 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
145 <option value="anidulans">Aspergillus nidulans (anidulans)</option> 110 <option value="aspergillus_nidulans">Aspergillus nidulans</option>
146 <option value="aspergillus_nidulans">Aspergillus nidulans (aspergillus_nidulans)</option>
147 <option value="aspergillus_oryzae">Aspergillus oryzae</option> 111 <option value="aspergillus_oryzae">Aspergillus oryzae</option>
148 <option value="aspergillus_terreus">Aspergillus terreus</option> 112 <option value="aspergillus_terreus">Aspergillus terreus</option>
113 <option value="Aurelia_aurita">Aurelia aurita</option>
114 <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
115 <option value="Berviolum_minutum">Berviolum minutum</option>
116 <option value="bombus_impatiens1">Bombus impatiens1</option>
117 <option value="bombus_terrestris2">Bombus terrestris2</option>
149 <option value="botrytis_cinerea">Botrytis cinerea</option> 118 <option value="botrytis_cinerea">Botrytis cinerea</option>
119 <option value="b_pseudomallei">Burkholderia pseudomallei (b_pseudomallei)</option>
120 <option value="Branchiostoma_floridae">Branchiostoma floridae</option>
121 <option value="brugia">Brugia malayi (brugia)</option>
122 <option value="cacao">(cacao)</option>
123 <option value="caenorhabditis">Caenorhabditis elegans (caenorhabditis)</option>
124 <option value="camponotus_floridanus">Camponotus floridanus</option>
150 <option value="candida_albicans">Candida albicans</option> 125 <option value="candida_albicans">Candida albicans</option>
151 <option value="candida_guilliermondii">Candida guilliermondii</option> 126 <option value="candida_guilliermondii">Candida guilliermondii</option>
152 <option value="candida_tropicalis">Candida tropicalis</option> 127 <option value="candida_tropicalis">Candida tropicalis</option>
128 <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
129 <!-- <option value="c_elegans_trsk">Caenorhabditis elegans</option> do not use according to augustus commit messages -->
153 <option value="chaetomium_globosum">Chaetomium globosum</option> 130 <option value="chaetomium_globosum">Chaetomium globosum</option>
131 <option value="chicken">Gallus gallus (chicken)</option>
132 <option value="chiloscyllium">Chiloscyllium punctatum (chiloscyllium)</option>
133 <option value="chlamy2011">chlamy2011</option>
134 <option value="chlamydomonas">Chlamydomonas reinhardtii (chlamydomonas)</option>
135 <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option>
136 <option value="chlorella">chlorella</option>
137 <option value="Chloropicon_primus">Chloropicon primus</option>
138 <option value="Chrysaora_chesapeakei">Chrysaora chesapeakei</option>
139 <option value="ciona">ciona</option>
154 <option value="coccidioides_immitis">Coccidioides immitis</option> 140 <option value="coccidioides_immitis">Coccidioides immitis</option>
155 <option value="coprinus">Coprinus cinereus (coprinus)</option> 141 <option value="Conidiobolus_coronatus">Conidiobolus coronatus</option>
156 <option value="coprinus_cinereus">Coprinus cinereus (coprinus_cinereus)</option> 142 <option value="coprinus">coprinus</option>
143 <option value="coprinus_cinereus">Coprinus cinereus</option>
144 <option value="coyote_tobacco">Coyote tobacco</option>
145 <option value="cryptococcus">cryptococcus</option>
157 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> 146 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
158 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option> 147 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
159 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option> 148 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
160 <option value="cryptococcus">Cryptococcus neoformans (cryptococcus)</option> 149 <option value="Cryptosporidium_hominis">Cryptosporidium hominis</option>
161 <option value="cryptococcus_neoformans">Cryptococcus neoformans (cryptococcus_neoformans)</option> 150 <option value="culex">culex</option>
151 <option value="Cyclotella_cryptica">Cyclotella cryptica</option>
162 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> 152 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
153 <option value="Dermasterias_imbricata">Dermasterias imbricata</option>
154 <option value="Dunaliella_salina">Dunaliella salina</option>
155 <option value="E_coli_K12">Escherichia K12 (E_coli_K12)</option>
156 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
157 <option value="elephant_shark">Callorhinchus milii (elephant_shark)</option>
163 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option> 158 <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
164 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option> 159 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
165 <option value="eremothecium_gossypii">Eremothecium gossypii</option> 160 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
161 <option value="Fistulifera_solaris">Fistulifera solaris</option>
162 <option value="fly">Drosophila melanogaster (fly)</option>
163 <option value="fly_exp">Drosophila melanogaster (fly) experimental parameters</option>
164 <option value="Fragilariopsis_cylindrus_CCMP1102">Fragilariopsis cylindrus CCMP1102</option>
165 <option value="fusarium">fusarium</option>
166 <option value="fusarium_graminearum">Fusarium graminearum</option> 166 <option value="fusarium_graminearum">Fusarium graminearum</option>
167 <option value="histoplasma_capsulatum">Histoplasma capsulatum (histoplasma_capsulatum)</option> 167 <option value="galdieria">Galdieria sulphuraria (galdieria)</option>
168 <option value="histoplasma">Histoplasma capsulatum (histoplasma)</option> 168 <option value="generic">generic</option>
169 <option value="gigaspora_margarita">Gigaspora margarita</option>
170 <option value="Gonapodya_prolifera">Gonapodya prolifera</option>
171 <option value="heliconius_melpomene1">Heliconius melpomene1</option>
172 <option value="histoplasma">histoplasma</option>
173 <option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
174 <option value="honeybee1">Apis mellifera (honeybee1)</option>
175 <option value="human">Homo sapiens (human)</option>
176 <option value="Hydra_vulgaris">Hydra vulgaris</option>
177 <option value="hymenolepis_microstoma">Hymenolepis microstoma</option>
178 <option value="japaneselamprey">Lethenteron camtschaticum (japaneselamprey)</option>
169 <option value="kluyveromyces_lactis">Kluyveromyces lactis</option> 179 <option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
170 <option value="laccaria_bicolor">Laccaria bicolor</option> 180 <option value="laccaria_bicolor">Laccaria bicolor</option>
171 <option value="lamprey">Petromyzon marinus</option>
172 <option value="leishmania_tarentolae">Leishmania tarentolae</option> 181 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
182 <option value="Leptasterias_sp">Leptasterias sp</option>
183 <option value="Loa_loa">Loa loa</option>
173 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> 184 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
174 <option value="magnaporthe_grisea">Magnaporthe grisea</option> 185 <option value="magnaporthe_grisea">Magnaporthe grisea</option>
186 <option value="maize">Zea mays (maize)</option>
187 <option value="maize5">Zea mays (maize5)</option>
188 <option value="Micromonas_commoda">Micromonas commoda</option>
189 <option value="Micromonas_pusilla">Micromonas pusilla</option>
190 <option value="mnemiopsis_leidyi">Mnemiopsis leidyi</option>
191 <option value="Monoraphidium_neglectum">Monoraphidium neglectum</option>
192 <option value="Monosiga_brevicollis">Monosiga brevicollis</option>
193 <option value="Naegleria_gruberi">Naegleria gruberi</option>
194 <option value="nasonia">Nasonia vitripennis (nasonia)</option>
195 <option value="nematostella_vectensis">Nematostella vectensis</option>
196 <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
197 <option value="neurospora">neurospora</option>
175 <option value="neurospora_crassa">Neurospora crassa</option> 198 <option value="neurospora_crassa">Neurospora crassa</option>
199 <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
200 <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp lucimarinus</option>
201 <option value="Ostreococcus_tauri">Ostreococcus tauri</option>
202 <option value="Paramecium_tetraurelia">Paramecium tetraurelia</option>
203 <option value="parasteatoda">Parasteatoda tepidariorum (parasteatoda)</option>
204 <option value="pchrysosporium">Phanerochaete chrysosporium (pchrysosporium)</option>
205 <option value="pea_aphid">Acyrthosiphon pisum (pea_aphid)</option>
206 <option value="Pediculus_humanus">Pediculus humanus</option>
207 <option value="Perkinsus_marinus">Perkinsus marinus</option>
208 <option value="pfalciparum">Plasmodium falciparum (pfalciparum)</option>
209 <option value="Phaeodactylum_tricornutum">Phaeodactylum tricornutum</option>
176 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> 210 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
211 <option value="Physcomitrium_patens">Physcomitrium patens</option>
177 <option value="pichia_stipitis">Pichia stipitis</option> 212 <option value="pichia_stipitis">Pichia stipitis</option>
213 <option value="pisaster">Pisaster ochraceus (pisaster)</option>
214 <option value="pneumocystis">pneumocystis</option>
215 <option value="Populus_trichocarpa">Populus trichocarpa</option>
216 <option value="Pseudo-nitzschia_multistriata">Pseudo-nitzschia multistriata</option>
217 <option value="Ptychodera_flava">Ptychodera flava</option>
218 <option value="Pycnopodia_helianthoides">Pycnopodia helianthoides</option>
219 <option value="Raphidocelis_subcapitata">Raphidocelis subcapitata</option>
220 <option value="rhincodon">Rhincodon typus (rhincodon)</option>
178 <option value="rhizopus_oryzae">Rhizopus oryzae</option> 221 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
179 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae saccharomyces_cerevisiae_S288C</option> 222 <option value="rhodnius">Rhodnius</option>
180 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae RM11-1a-1</option> 223 <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
181 <option value="saccharomyces">Saccharomyces cerevisiae (saccharomyces)</option> 224 <option value="rice">Oryza (rice)</option>
225 <option value="Ricinus_communis">Ricinus communis</option>
226 <option value="saccharomyces">Saccharomyces</option>
227 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a 1</option>
228 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
229 <option value="s_aureus">Staphylococcus aureus (s_aureus)</option>
230 <option value="schistosoma">Schistosoma mansoni (schistosoma)</option>
231 <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
182 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> 232 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
183 <option value="trichinella">Trichinella spiralis</option> 233 <option value="Sclerotinia_sclerotiorum">Sclerotinia sclerotiorum</option>
184 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> 234 <option value="scyliorhinus">Scyliorhinus torazame (scyliorhinus)</option>
185 <option value="nasonia">Nasonia vitripennis</option> 235 <option value="sealamprey">Petromyzon marinus (sealamprey)</option>
186 <option value="tomato">Solanum lycopersicum</option> 236 <option value="Skeletonema_costatum">Skeletonema costatum</option>
187 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
188 <option value="amphimedon">Amphimedon queenslandica</option>
189 <option value="pneumocystis">Pneumocystis jirovecii</option>
190 <option value="chicken">Gallus gallus domesticus (chicken)</option>
191 <option value="cacao">Theobroma cacao (cacao)</option>
192 <option value="heliconius_melpomene1">Heliconius melpomene</option>
193 <option value="xenoturbella">Xenoturbella</option>
194 <option value="E_coli_K12">Escherichia coli K12</option>
195 <option value="c_elegans_trsk">c elegans trsk</option>
196 <option value="camponotus_floridanus">Camponotus floridanus</option>
197 <option value="coyote_tobacco">Coyote tobacco</option>
198 <option value="s_aureus">Staphylococcus aureus</option>
199 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
200 <option value="wheat">Triticum aestivum</option>
201 <option value="zebrafish">Danio rerio</option>
202 <option value="bombus_impatiens1">Bombus impatiens1</option>
203 <option value="bombus_terrestris2">Bombus terrestris2</option>
204 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
205 <option value="culex_pipiens">Culex pipiens</option>
206 <option value="elephant_shark">Callorhinchus milii</option>
207 <option value="honeybee1">Apis mellifera</option>
208 <option value="pea_aphid">Acyrthosiphon pisum</option>
209 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
210 <option value="ustilago_maydis">Ustilago maydis</option>
211 <option value="verticillium_albo_atrum1">Verticillium albo-atrum</option>
212 <option value="verticillium_longisporum1">Verticillium longisporum</option>
213 <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
214 <option value="adorsata">Apis dorsata</option>
215 <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
216 <option value="maker2_athal1">Arabidopsis thaliana (maker2_athal1)</option>
217 <option value="maker2_c_elegans1">Caenorhabditis elegans (maker2_c_elegans1)</option>
218 <option value="maker2_spomb1">Saccharomyces cerevisiae (maker2_spomb1)</option>
219 <option value="parasteatoda">Parasteatoda SP.</option>
220 <option value="rice">Oryza sp.</option>
221 <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
222 <option value="Ptychodera_flava">Ptychodera flava</option>
223 <option value="Argopecten_irridians">Argopecten irridians</option>
224 <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
225 <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
226 <option value="Chrysaora_chesapeakeij">Chrysaora chesapeakeij</option>
227 <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
228 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
229 <option value="Aurelia_aurita">Aurelia aurita</option>
230 <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
231 <option value="Gonapodya_prolifera">Dunaliella salina</option>
232 <option value="Sordaria_macrospora">Sordaria macrospora</option> 237 <option value="Sordaria_macrospora">Sordaria macrospora</option>
233 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option> 238 <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
239 <option value="s_pneumoniae">Streptococcus pneumoniae (s_pneumoniae)</option>
240 <option value="strongylocentrotus_purpuratus">Strongylocentrotus purpuratus</option>
241 <option value="sulfolobus_solfataricus">Sulfolobus solfataricus</option>
242 <option value="sunflower">Helianthus annuus (sunflower)</option>
243 <option value="Taeniopygia_guttata">Taeniopygia guttata</option>
244 <option value="template_prokaryotic">Template prokaryotic</option>
245 <option value="tetrahymena">tetrahymena</option>
246 <option value="Thalassiosira_pseudonana_CCMP1335">Thalassiosira pseudonana CCMP1335</option>
247 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
248 <option value="tomato">Solanum lycopersicum (tomato)</option>
249 <option value="toxoplasma">Toxoplasma gondii (toxoplasma)</option>
250 <option value="tribolium2012">tribolium2012</option>
251 <option value="trichinella">Trichinella</option>
252 <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
253 <option value="Trypanosoma_cruzi">Trypanosoma cruzi</option>
254 <option value="ustilago">Ustilago</option>
255 <option value="ustilago_maydis">Ustilago maydis</option>
256 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
257 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
258 <option value="Vitis_vinifera">Vitis vinifera</option>
234 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option> 259 <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option>
235 <option value="Monoraphidium_neglectum">Monoraphidium_neglectum</option> 260 <option value="volvox">volvox</option>
236 <option value="Raphidocelis_subcapita">Raphidocelis subcapita</option> 261 <option value="wheat">wheat</option>
237 <option value="Ostreococcus_tauri">Ostreococcus tauri</option> 262 <option value="Xenopus_tropicalis">Xenopus tropicalis</option>
238 <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp. lucimarinus</option> 263 <option value="Xiphophorus_maculatus">Xiphophorus maculatus</option>
239 <option value="Micromonas_pusilla">Micromonas pusilla</option> 264 <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
240 <option value="Micromonas_commoda">Micromonas commoda</option> 265 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
241 <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option> 266 <option value="zebrafish">Danio rerio (zebrafish)</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>
249 </param> 267 </param>
250 </when> 268 </when>
251 </conditional> 269 </conditional>
252 270
253 <param type="boolean" argument="--softmasking" 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." />
254 label="Softmasking" 272 <param type="select" argument="--strand" label="Predict genes on specific strands">
255 truevalue="1" falsevalue="0" checked="true"
256 help="If this option is enabled, lowercase letters are considered as repeated regions." />
257
258
259 <param type="select" argument="--strand"
260 label="Predict genes on specific strands">
261 <option value="both">both</option> 273 <option value="both">both</option>
262 <option value="forward">forward</option> 274 <option value="forward">forward</option>
263 <option value="backward">backward</option> 275 <option value="backward">backward</option>
264 </param> 276 </param>
265
266 <param argument="--genemodel" label="Gene Model" type="select" 277 <param argument="--genemodel" label="Gene Model" type="select"
267 help="Gene Model to predict, for more information please refer to the help."> 278 help="Gene Model to predict, for more information please refer to the help.">
268 <option value="complete">complete</option> 279 <option value="complete">complete</option>
269 <option value="partial">partial</option> 280 <option value="partial">partial</option>
270 <option value="intronless">intronless</option> 281 <option value="intronless">intronless</option>
271 <option value="atleastone">atleastone</option> 282 <option value="atleastone">atleastone</option>
272 <option value="exactlyone">exactlyone</option> 283 <option value="exactlyone">exactlyone</option>
273 </param> 284 </param>
274
275 <conditional name="hints"> 285 <conditional name="hints">
276 <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio"> 286 <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
277 <option value="F">No</option> 287 <option value="F">No</option>
278 <option value="T">Yes</option> 288 <option value="T">Yes</option>
279 </param> 289 </param>
284 help="A .cfg file listing hint sources and their boni and mali"/> 294 help="A .cfg file listing hint sources and their boni and mali"/>
285 </when> 295 </when>
286 <when value="F"> 296 <when value="F">
287 </when> 297 </when>
288 </conditional> 298 </conditional>
289
290 <conditional name="range"> 299 <conditional name="range">
291 <param name="userange" label="Specify prediction sequence range?" type="select" display="radio"> 300 <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
292 <option value="F">No</option> 301 <option value="F">No</option>
293 <option value="T">Yes</option> 302 <option value="T">Yes</option>
294 </param> 303 </param>
299 help="The end of the search range; must be greater than starting position"/> 308 help="The end of the search range; must be greater than starting position"/>
300 </when> 309 </when>
301 <when value="F"> 310 <when value="F">
302 </when> 311 </when>
303 </conditional> 312 </conditional>
304 313 <param name="gff" argument="--gff3" type="boolean" label="GFF formated output" help="Standard output is GTF." truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
305 <param name="gff" argument="--gff3" type="boolean" label="GFF formated output" 314 <param name="outputs" type="select" optional="true" multiple="true" label="Output options">
306 help="Standard output is GTF." 315 <option value="protein" selected="true">predicted protein sequences (--protein)</option>
307 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> 316 <option value="codingseq" selected="true">coding sequence as comment in the output file (--codingseq)</option>
308
309 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
310 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
311 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
312 <option value="introns">predicted intron sequences (--introns)</option> 317 <option value="introns">predicted intron sequences (--introns)</option>
313 <option value="start">predicted start codons (--start)</option> 318 <option value="start">predicted start codons (--start)</option>
314 <option value="stop">predicted stop codons (--stop)</option> 319 <option value="stop">predicted stop codons (--stop)</option>
315 <option value="cds" selected="true">CDS region (--cds)</option> 320 <option value="cds" selected="true">CDS region (--cds)</option>
316 </param> 321 </param>
320 <change_format> 325 <change_format>
321 <when input="gff" value="--gff3=on" format="gff3" /> 326 <when input="gff" value="--gff3=on" format="gff3" />
322 </change_format> 327 </change_format>
323 </data> 328 </data>
324 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence"> 329 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
325 <filter>'protein' in outputs</filter> 330 <filter>outputs and 'protein' in outputs</filter>
326 </data> 331 </data>
327 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence"> 332 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
328 <filter>'codingseq' in outputs</filter> 333 <filter>outputs and 'codingseq' in outputs</filter>
329 </data> 334 </data>
330 </outputs> 335 </outputs>
331 <tests> 336 <tests>
332 <test expect_num_outputs="3"> 337 <test expect_num_outputs="3">
333 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 338 <param name="input_genome" value="human_augustus.fa.gz" ftype="fasta.gz" />
334 <param name="organism" value="human" /> 339 <conditional name="model">
340 <param name="organism" value="human" />
341 </conditional>
335 <param name="utr" value="True" /> 342 <param name="utr" value="True" />
336 <param name="softmasking" value="False"/> 343 <param name="softmasking" value="False"/>
337 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/> 344 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
338 </test> 345 </test>
339 <test expect_num_outputs="3"> 346 <test expect_num_outputs="3">
340 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 347 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
341 <param name="organism" value="human" /> 348 <conditional name="model">
349 <param name="organism" value="human" />
350 </conditional>
342 <param name="utr" value="True" /> 351 <param name="utr" value="True" />
343 <param name="gff" value="True" /> 352 <param name="gff" value="True" />
344 <param name="softmasking" value="False"/> 353 <param name="softmasking" value="False"/>
345 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/> 354 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
346 </test> 355 </test>
347 <test expect_num_outputs="3"> 356 <test expect_num_outputs="3">
348 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 357 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
349 <param name="organism" value="human" /> 358 <conditional name="model">
359 <param name="organism" value="human" />
360 </conditional>
350 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" /> 361 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
351 <param name="softmasking" value="False"/> 362 <param name="softmasking" value="False"/>
352 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/> 363 <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" /> 364 <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" /> 365 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
355 </test> 366 </test>
356 <test expect_num_outputs="1"> 367 <test expect_num_outputs="1">
357 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" /> 368 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
358 <param name="organism" value="fly" /> 369 <conditional name="model">
359 <param name="usehints" value="T" /> 370 <param name="organism" value="fly" />
360 <param name="hintsfile" value="hints.truncated.adjusted.gff" /> 371 </conditional>
361 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> 372 <conditional name="hints">
362 <param name="outputs" value="" /> 373 <param name="usehints" value="T" />
374 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
375 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
376 </conditional>
377 <param name="outputs" value_json="null" />
363 <param name="softmasking" value="False"/> 378 <param name="softmasking" value="False"/>
364 <param name="outputs" value=""/> 379 <param name="outputs" value=""/>
365 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12"> 380 <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
366 <assert_contents> 381 <assert_contents>
367 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" /> 382 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
370 </output> 385 </output>
371 386
372 </test> 387 </test>
373 <test expect_num_outputs="1"> 388 <test expect_num_outputs="1">
374 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" /> 389 <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
375 <param name="organism" value="fly" /> 390 <conditional name="model">
376 <param name="usehints" value="T" /> 391 <param name="organism" value="fly" />
377 <param name="hintsfile" value="hints.truncated.adjusted.gff" /> 392 </conditional>
378 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> 393 <conditional name="hints">
379 <param name="userange" value="T" /> 394 <param name="usehints" value="T" />
380 <param name="start" value="7000" /> 395 <param name="hintsfile" value="hints.truncated.adjusted.gff" />
381 <param name="stop" value="9000" /> 396 <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
382 <param name="outputs" value="" /> 397 </conditional>
398 <conditional name="range">
399 <param name="userange" value="T" />
400 <param name="start" value="7000" />
401 <param name="stop" value="9000" />
402 </conditional>
403 <param name="outputs" value_json="null" />
383 <param name="softmasking" value="False"/> 404 <param name="softmasking" value="False"/>
384 <param name="outputs" value=""/> 405 <param name="outputs" value_json="null"/>
385 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12"> 406 <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
386 <assert_contents> 407 <assert_contents>
387 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" /> 408 <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
388 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" /> 409 <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
389 </assert_contents> 410 </assert_contents>
390 </output> 411 </output>
391 </test> 412 </test>
392 <!-- Test softmasking parameter--> 413 <!-- Test softmasking parameter-->
393 <test expect_num_outputs="1"> 414 <test expect_num_outputs="1">
394 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 415 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
395 <param name="organism" value="human" /> 416 <conditional name="model">
417 <param name="organism" value="human" />
418 </conditional>
396 <param name="utr" value="True" /> 419 <param name="utr" value="True" />
397 <param name="softmasking" value="True"/> 420 <param name="softmasking" value="True"/>
398 <param name="outputs" value=""/> 421 <param name="outputs" value_json="null"/>
399 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/> 422 <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
400 </test> 423 </test>
401 424
402 </tests> 425 </tests>
403 <help> 426 <help>