Mercurial > repos > bgruening > augustus

comparison augustus.xml @ 3:f5075dee9d6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
author iuc
date Fri, 22 May 2015 04:55:25 -0400
parents a77a4e9921e0
children 4de31938431b
comparison
equal deleted inserted replaced
2:a77a4e9921e0 3:f5075dee9d6b
1 <tool id="augustus" name="Augustus" version="0.3.1"> 1 <tool id="augustus" name="Augustus" version="3.1.0">
2 <description>gene prediction for eukaryotic genomes</description> 2 <description>gene prediction for 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 <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.7">augustus</requirement> 5 <requirement type="package" version="3.1">augustus</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
10 <regex match="Error:" /> 10 <regex match="Error:" />
11 <regex match="Exception:" /> 11 <regex match="Exception:" />
12 </stdio> 12 </stdio>
13 <command> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config 15 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
16 ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed 16 ## script is used to extract the sequences into additional files
17 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files
18 17
19 augustus 18 augustus
20 --strand=$strand 19 --strand=$strand
21 $noInFrameStop 20 $noInFrameStop
22 $gff 21 $gff
22 --uniqueGeneId=true
23 23
24 #if 'protein' in str($outputs).split(','): 24 #if 'protein' in str($outputs).split(','):
25 --protein=on 25 --protein=on
26 #else: 26 #else:
27 --protein=off 27 --protein=off
57 --cds=off 57 --cds=off
58 #end if 58 #end if
59 59
60 $singlestrand 60 $singlestrand
61 $input_genome 61 $input_genome
62 $mea
63 $utr 62 $utr
64 --genemodel=$genemodel 63 --genemodel=$genemodel
65 --species=$organism 64 --species=$organism
66 ##--outfile=$output 65
67 | tee $output 66 | tee $output
68 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','): 67 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
69 | python $__tool_directory__/extract_features.py 68 | python $__tool_directory__/extract_features.py
70 #if 'protein' in str($outputs).split(','): 69 #if 'protein' in str($outputs).split(','):
71 --protein $protein_output 70 --protein $protein_output
76 #end if 75 #end if
77 ]]> 76 ]]>
78 </command> 77 </command>
79 <inputs> 78 <inputs>
80 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> 79 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
81 <param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons (--noInFrameStop)" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur" /> 80 <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"
82 <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands (--singlestrand)" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> 81 label="Don't report transcripts with in-frame stop codons (--noInFrameStop)"
83 <param name="mea" type="boolean" label="Using the maximum expected accuracy approach (--mea)" truevalue="--mea=1" falsevalue="" checked="false" help="MEA is an alternative decoding approach." /> 82 truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
84 <param name="utr" type="boolean" label="Predict the untranslated regions in addition to the coding sequence (--UTR)" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." /> 83 help="Otherwise, intron-spanning stop codons could occur. (--noInFrameStop)" />
84 <param name="singlestrand" type="boolean" argument="--singlestrand"
85 label="Predict genes independently on each strand"
86 help="This allows overlapping genes on opposite strands. (--singlestrand)"
87 truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
88
89 <param name="utr" type="boolean" argument="--UTR"
90 label="Predict the untranslated regions in addition to the coding sequence"
91 truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
92 help="This currently works only for human, galdieria, toxoplasma and caenorhabditis. (--UTR)" />
85 93
86 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> 94 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
87 <option value="human">Homo sapiens</option> 95 <option value="human">Homo sapiens</option>
88 <option value="fly">Drosophila melanogaster</option> 96 <option value="fly">Drosophila melanogaster</option>
89 <option value="arabidopsis">Arabidopsis thaliana</option> 97 <option value="arabidopsis">Arabidopsis thaliana</option>
92 <option value="tribolium2012">Tribolium castaneum</option> 100 <option value="tribolium2012">Tribolium castaneum</option>
93 <option value="schistosoma">Schistosoma mansoni</option> 101 <option value="schistosoma">Schistosoma mansoni</option>
94 <option value="tetrahymena">Tetrahymena thermophila</option> 102 <option value="tetrahymena">Tetrahymena thermophila</option>
95 <option value="galdieria">Galdieria sulphuraria</option> 103 <option value="galdieria">Galdieria sulphuraria</option>
96 <option value="maize">Zea mays</option> 104 <option value="maize">Zea mays</option>
97 <option value="toxoplasma ">Toxoplasma gondii</option> 105 <option value="toxoplasma">Toxoplasma gondii</option>
98 <option value="caenorhabditis ">Caenorhabditis elegans</option> 106 <option value="caenorhabditis ">Caenorhabditis elegans</option>
99 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> 107 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
100 <option value="aspergillus_nidulans ">Aspergillus nidulans</option> 108 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
101 <option value="aspergillus_oryzae ">Aspergillus oryzae</option> 109 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
102 <option value="aspergillus_terreus">Aspergillus terreus</option> 110 <option value="aspergillus_terreus">Aspergillus terreus</option>
103 <option value="botrytis_cinerea ">Botrytis cinerea</option> 111 <option value="botrytis_cinerea ">Botrytis cinerea</option>
104 <option value="candida_albicans ">Candida albicans</option> 112 <option value="candida_albicans ">Candida albicans</option>
105 <option value="candida_guilliermondii ">Candida guilliermondii</option> 113 <option value="candida_guilliermondii ">Candida guilliermondii</option>
106 <option value="candida_tropicalis ">Candida tropicalis</option> 114 <option value="candida_tropicalis ">Candida tropicalis</option>
107 <option value="chaetomium_globosum">Chaetomium globosum</option> 115 <option value="chaetomium_globosum">Chaetomium globosum</option>
108 <option value="coccidioides_immitis ">Coccidioides immitis</option> 116 <option value="coccidioides_immitis">Coccidioides immitis</option>
109 <option value="coprinus ">Coprinus cinereus</option> 117 <option value="coprinus">Coprinus cinereus</option>
110 <option value="coprinus_cinereus">Coprinus cinereus</option> 118 <option value="coprinus_cinereus">Coprinus cinereus</option>
111 <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option> 119 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
112 <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option> 120 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
113 <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option> 121 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
122 <option value="cryptococcus">Cryptococcus neoformans</option>
114 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> 123 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
115 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> 124 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
116 <option value="eremothecium_gossypii">Eremothecium gossypii</option> 125 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
117 <option value="fusarium_graminearum ">Fusarium graminearum</option> 126 <option value="fusarium_graminearum ">Fusarium graminearum</option>
118 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> 127 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
119 <option value="(histoplasma)">Histoplasma capsulatum</option> 128 <option value="histoplasma">Histoplasma capsulatum</option>
120 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> 129 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
121 <option value="laccaria_bicolor ">Laccaria bicolor</option> 130 <option value="laccaria_bicolor ">Laccaria bicolor</option>
122 <option value="lamprey">Petromyzon marinus</option> 131 <option value="lamprey">Petromyzon marinus</option>
123 <option value="leishmania_tarentolae">Leishmania tarentolae</option> 132 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
124 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> 133 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
125 <option value="magnaporthe_grisea ">Magnaporthe grisea</option> 134 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
126 <option value="neurospora_crassa">Neurospora crassa</option> 135 <option value="neurospora_crassa">Neurospora crassa</option>
127 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> 136 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
128 <option value="pichia_stipitis">Pichia stipitis</option> 137 <option value="pichia_stipitis">Pichia stipitis</option>
129 <option value="rhizopus_oryzae">Rhizopus oryzae</option> 138 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
130 <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option> 139 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
131 <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option> 140 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
132 <option value="(saccharomyces)">Saccharomyces cerevisiae</option> 141 <option value="saccharomyces">Saccharomyces cerevisiae</option>
133 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> 142 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
134 <option value="trichinella">Trichinella spiralis</option> 143 <option value="trichinella">Trichinella spiralis</option>
135 <option value="ustilago_maydis">Ustilago maydis</option> 144 <option value="ustilago_maydis">Ustilago maydis</option>
136 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> 145 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
137 <option value="nasonia">Nasonia vitripennis</option> 146 <option value="nasonia">Nasonia vitripennis</option>
141 <option value="pneumocystis">Pneumocystis jirovecii</option> 150 <option value="pneumocystis">Pneumocystis jirovecii</option>
142 <option value="chicken">Gallus gallus domesticus (chicken)</option> 151 <option value="chicken">Gallus gallus domesticus (chicken)</option>
143 <option value="cacao">Theobroma cacao (cacao)</option> 152 <option value="cacao">Theobroma cacao (cacao)</option>
144 <option value="heliconius_melpomene1">Heliconius melpomene</option> 153 <option value="heliconius_melpomene1">Heliconius melpomene</option>
145 <option value="xenoturbella">Xenoturbella</option> 154 <option value="xenoturbella">Xenoturbella</option>
146 </param> 155 <option value="E_coli_K12">E coli K12</option>
147 156 <option value="c_elegans_trsk">c elegans trsk</option>
148 <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand."> 157 <option value="camponotus_floridanus">Camponotus floridanus</option>
158 <option value="coyote_tobacco">Coyote tobacco</option>
159 <option value="s_aureus">Staphylococcus aureus</option>
160 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
161 <option value="wheat">wheat</option>
162 <option value="zebrafish">Danio rerio</option>
163 <option value="anidulans">Aspergillus nidulans</option>
164 <option value="bombus_impatiens1">Bombus impatiens1</option>
165 <option value="bombus_terrestris2">Bombus terrestris2</option>
166 <option value="botrytis_cinerea">Botrytis cinerea</option>
167 <option value="brugia_malayi">Brugia malayi</option>
168 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
169 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
170 <option value="culex_pipiens">Culex pipiens</option>
171 <option value="elephant_shark">Callorhinchus milii</option>
172 <option value="honeybee1">Apis mellifera</option>
173 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
174 <option value="pea_aphid">Acyrthosiphon pisum</option>
175 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
176 <option value="ustilago_maydis">Ustilago maydis</option>
177 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
178 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
179 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
180 <option value="adorsata">adorsata</option>
181 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
182 <option value="maker2_athal1">maker2_athal1</option>
183 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
184 <option value="maker2_dmel1">maker2_dmel1</option>
185 <option value="maker2_spomb1">maker2_spomb1</option>
186 <option value="parasteatoda">parasteatoda</option>
187 <option value="rice">rice</option>
188 <option value="schistosoma2">schistosoma2</option>
189 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
190 </param>
191
192 <param name="strand" type="select" argument="--strand"
193 label="Predict genes on specific strands" help="(--strand)">
149 <option value="both">both</option> 194 <option value="both">both</option>
150 <option value="forward">forward</option> 195 <option value="forward">forward</option>
151 <option value="backward">backward</option> 196 <option value="backward">backward</option>
152 </param> 197 </param>
153 198
154 <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help."> 199 <param name="genemodel" label="Gene Model" type="select"
200 help="Gene Model to predict, for more information please refere to the help. (--genemodel)">
155 <option value="complete">complete</option> 201 <option value="complete">complete</option>
156 <option value="partial">partial</option> 202 <option value="partial">partial</option>
157 <option value="intronless">intronless</option> 203 <option value="intronless">intronless</option>
158 <option value="atleastone">atleastone</option> 204 <option value="atleastone">atleastone</option>
159 <option value="exactlyone">exactlyone</option> 205 <option value="exactlyone">exactlyone</option>
160 <option value="bacterium">bacterium (beta version)</option>
161 </param> 206 </param>
162 207
163 208 <param name="gff" type="boolean" label="GFF formated output"
164 <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> 209 help="Standard output is GTF. (--gff3)"
210 truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
165 211
166 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> 212 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
167 <option value="protein" selected="True">predicted protein sequences (--protein)</option> 213 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
168 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option> 214 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
169 <option value="introns">predicted intron sequences (--introns)</option> 215 <option value="introns">predicted intron sequences (--introns)</option>
172 <option value="cds" selected="true">CDS region (--cds)</option> 218 <option value="cds" selected="true">CDS region (--cds)</option>
173 219
174 <validator type="no_options" message="Please select at least one output file." /> 220 <validator type="no_options" message="Please select at least one output file." />
175 </param> 221 </param>
176 222
177
178 </inputs> 223 </inputs>
179 <outputs> 224 <outputs>
180 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF"> 225 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
181 <change_format> 226 <change_format>
182 <when input="gff" value="--gff3=on" format="gff" /> 227 <when input="gff" value="--gff3=on" format="gff3" />
183 </change_format> 228 </change_format>
184 </data> 229 </data>
185 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence"> 230 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
186 <filter>'protein' in outputs</filter> 231 <filter>'protein' in outputs</filter>
187 </data> 232 </data>
191 </outputs> 236 </outputs>
192 <tests> 237 <tests>
193 <test> 238 <test>
194 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 239 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
195 <param name="organism" value="human" /> 240 <param name="organism" value="human" />
196 <param name="utr" value="--UTR=on" /> 241 <param name="utr" value="True" />
197 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/> 242 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
198 </test> 243 </test>
199 <test> 244 <test>
200 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 245 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
201 <param name="organism" value="human" /> 246 <param name="organism" value="human" />
202 <param name="utr" value="--UTR=on" /> 247 <param name="utr" value="True" />
203 <param name="gff" value="--gff3=on" /> 248 <param name="gff" value="True" />
204 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/> 249 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
205 </test>
206 <test>
207 <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
208 <param name="organism" value="arabidopsis" />
209 <param name="singlestrand" value="--singlestrand=true" />
210 <param name="mea" value="--mea=1" />
211 <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>
212 </test> 250 </test>
213 <test> 251 <test>
214 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 252 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
215 <param name="organism" value="human" /> 253 <param name="organism" value="human" />
216 <param name="outputs" value="protein,codingseq,introns,cds" /> 254 <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
217 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/> 255 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
218 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> 256 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
219 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> 257 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
220 </test> 258 </test>
221 </tests> 259 </tests>
222 <help> 260 <help>