Mercurial > repos > bgruening > augustus
comparison augustus.xml @ 0:af307d3285c5 draft
Uploaded
author | bgruening |
---|---|
date | Sat, 06 Jul 2013 10:07:41 -0400 (2013-07-06) |
parents | |
children | e2b822d7408f |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:af307d3285c5 |
---|---|
1 <tool id="augustus" name="Augustus" version="0.3"> | |
2 <description>gene prediction for eukaryotic genomes</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.7">augustus</requirement> | |
5 <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement> | |
6 </requirements> | |
7 <command> | |
8 ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config | |
9 ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed | |
10 ## 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 | |
11 | |
12 augustus | |
13 --strand=$strand | |
14 $noInFrameStop | |
15 $gff | |
16 $protein | |
17 $introns | |
18 $start | |
19 $stop | |
20 $cds | |
21 $codingseq | |
22 $singlestrand | |
23 $input_genome | |
24 $mea | |
25 $utr | |
26 --genemodel=$genemodel | |
27 --species=$organism | |
28 ##--outfile=$output | |
29 | tee $output | |
30 #if $protein or $codingseq: | |
31 | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py | |
32 #if $protein: | |
33 --protein $protein_output | |
34 #end if | |
35 #if $codingseq: | |
36 --codingseq $codingseq_output | |
37 #end if | |
38 #end if | |
39 </command> | |
40 <inputs> | |
41 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> | |
42 <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" /> | |
43 <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" /> | |
44 <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." /> | |
45 <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." /> | |
46 | |
47 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> | |
48 <option value="human">Homo sapiens</option> | |
49 <option value="fly">Drosophila melanogaster</option> | |
50 <option value="arabidopsis">Arabidopsis thaliana</option> | |
51 <option value="brugia ">Brugia malayi</option> | |
52 <option value="aedes">Aedes aegypti</option> | |
53 <option value="tribolium2012">Tribolium castaneum</option> | |
54 <option value="schistosoma">Schistosoma mansoni</option> | |
55 <option value="tetrahymena">Tetrahymena thermophila</option> | |
56 <option value="galdieria">Galdieria sulphuraria</option> | |
57 <option value="maize">Zea mays</option> | |
58 <option value="toxoplasma ">Toxoplasma gondii</option> | |
59 <option value="caenorhabditis ">Caenorhabditis elegans</option> | |
60 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> | |
61 <option value="aspergillus_nidulans ">Aspergillus nidulans</option> | |
62 <option value="aspergillus_oryzae ">Aspergillus oryzae</option> | |
63 <option value="aspergillus_terreus">Aspergillus terreus</option> | |
64 <option value="botrytis_cinerea ">Botrytis cinerea</option> | |
65 <option value="candida_albicans ">Candida albicans</option> | |
66 <option value="candida_guilliermondii ">Candida guilliermondii</option> | |
67 <option value="candida_tropicalis ">Candida tropicalis</option> | |
68 <option value="chaetomium_globosum">Chaetomium globosum</option> | |
69 <option value="coccidioides_immitis ">Coccidioides immitis</option> | |
70 <option value="coprinus ">Coprinus cinereus</option> | |
71 <option value="coprinus_cinereus">Coprinus cinereus</option> | |
72 <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option> | |
73 <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option> | |
74 <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option> | |
75 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> | |
76 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> | |
77 <option value="eremothecium_gossypii">Eremothecium gossypii</option> | |
78 <option value="fusarium_graminearum ">Fusarium graminearum</option> | |
79 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> | |
80 <option value="(histoplasma)">Histoplasma capsulatum</option> | |
81 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> | |
82 <option value="laccaria_bicolor ">Laccaria bicolor</option> | |
83 <option value="lamprey">Petromyzon marinus</option> | |
84 <option value="leishmania_tarentolae">Leishmania tarentolae</option> | |
85 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> | |
86 <option value="magnaporthe_grisea ">Magnaporthe grisea</option> | |
87 <option value="neurospora_crassa">Neurospora crassa</option> | |
88 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> | |
89 <option value="pichia_stipitis">Pichia stipitis</option> | |
90 <option value="rhizopus_oryzae">Rhizopus oryzae</option> | |
91 <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option> | |
92 <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option> | |
93 <option value="(saccharomyces)">Saccharomyces cerevisiae</option> | |
94 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> | |
95 <option value="trichinella">Trichinella spiralis</option> | |
96 <option value="ustilago_maydis">Ustilago maydis</option> | |
97 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> | |
98 <option value="nasonia">Nasonia vitripennis</option> | |
99 <option value="tomato">Solanum lycopersicum</option> | |
100 <option value="chlamydomonas">Chlamydomonas reinhardtii</option> | |
101 <option value="amphimedon">Amphimedon queenslandica</option> | |
102 <option value="pneumocystis">Pneumocystis jirovecii</option> | |
103 <option value="chicken">Gallus gallus domesticus (chicken)</option> | |
104 <option value="cacao">Theobroma cacao (cacao)</option> | |
105 <option value="heliconius_melpomene1">Heliconius melpomene</option> | |
106 <option value="xenoturbella">Xenoturbella</option> | |
107 </param> | |
108 | |
109 <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand."> | |
110 <option value="both">both</option> | |
111 <option value="forward">forward</option> | |
112 <option value="backward">backward</option> | |
113 </param> | |
114 | |
115 <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."> | |
116 <option value="complete">complete</option> | |
117 <option value="partial">partial</option> | |
118 <option value="intronless">intronless</option> | |
119 <option value="atleastone">atleastone</option> | |
120 <option value="exactlyone">exactlyone</option> | |
121 <option value="bacterium">bacterium (beta version)</option> | |
122 </param> | |
123 | |
124 <param name="protein" type="boolean" label="Output predicted protein sequences (--protein)" truevalue="--protein=on" falsevalue="--protein=off" checked="true" /> | |
125 <param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file (codingseq)" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="true" /> | |
126 <param name="introns" type="boolean" label="Output predicted intron sequences (--introns)" truevalue="--introns=on" falsevalue="--introns=off" checked="false" /> | |
127 <param name="start" type="boolean" label="Output predicted start codons (--start)" truevalue="--start=on" falsevalue="--start=off" checked="false" /> | |
128 <param name="stop" type="boolean" label="Output predicted stop codons (--stop)" truevalue="--stop=on" falsevalue="--stop=off" checked="false" /> | |
129 <param name="cds" type="boolean" label="Output CDS region (--cds)" truevalue="--cds=on" falsevalue="--cds=off" checked="true" /> | |
130 <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> | |
131 | |
132 </inputs> | |
133 <outputs> | |
134 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF"> | |
135 <change_format> | |
136 <when input="gff" value="--gff3=on" format="gff" /> | |
137 </change_format> | |
138 </data> | |
139 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence"> | |
140 <filter>protein == True</filter> | |
141 </data> | |
142 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence"> | |
143 <filter>codingseq == True</filter> | |
144 </data> | |
145 </outputs> | |
146 <tests> | |
147 <test> | |
148 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> | |
149 <param name="organism" value="human" /> | |
150 <param name="utr" value="--UTR=on" /> | |
151 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/> | |
152 </test> | |
153 <test> | |
154 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> | |
155 <param name="organism" value="human" /> | |
156 <param name="utr" value="--UTR=on" /> | |
157 <param name="gff" value="--gff3=on" /> | |
158 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/> | |
159 </test> | |
160 <test> | |
161 <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" /> | |
162 <param name="organism" value="arabidopsis" /> | |
163 <param name="singlestrand" value="--singlestrand=true" /> | |
164 <param name="mea" value="--mea=1" /> | |
165 <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/> | |
166 </test> | |
167 <test> | |
168 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> | |
169 <param name="organism" value="human" /> | |
170 <param name="protein" value="--protein=on" /> | |
171 <param name="codingseq" value="--codingseq=on" /> | |
172 <param name="introns" value="--introns=on" /> | |
173 <param name="cds" value="--cds=on" /> | |
174 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/> | |
175 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> | |
176 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> | |
177 </test> | |
178 </tests> | |
179 <help> | |
180 | |
181 **What it does** | |
182 | |
183 AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. | |
184 It can be used as an ab initio program, which means it bases its prediction purely on the | |
185 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources | |
186 such as EST, MS/MS, protein alignments and synthenic genomic alignments. | |
187 | |
188 ----- | |
189 | |
190 **Parameters** | |
191 | |
192 Gene Model:: | |
193 | |
194 partial : allow prediction of incomplete genes at the sequence boundaries (default) | |
195 intronless : only predict single-exon genes like in prokaryotes and some eukaryotes | |
196 complete : only predict complete genes | |
197 atleastone : predict at least one complete gene | |
198 exactlyone : predict exactly one complete gene | |
199 | |
200 | |
201 | |
202 **Example** | |
203 | |
204 Suppose you have the following DNA formatted sequences:: | |
205 | |
206 >Seq1 | |
207 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg | |
208 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag | |
209 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc | |
210 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc | |
211 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg | |
212 | |
213 Running this tool will produce this:: | |
214 | |
215 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- | |
216 # | |
217 # Constraints/Hints: | |
218 # (none) | |
219 # Predicted genes for sequence number 1 on both strands | |
220 # start gene g1 | |
221 scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6 | |
222 scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1 | |
223 scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6"; | |
224 scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6"; | |
225 scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6"; | |
226 scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6"; | |
227 scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6"; | |
228 scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6"; | |
229 scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6"; | |
230 scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6"; | |
231 scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6"; | |
232 scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6"; | |
233 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6"; | |
234 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6"; | |
235 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; | |
236 | |
237 | |
238 **References** | |
239 | |
240 Mario Stanke and Stephan Waack (2003) | |
241 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. | |
242 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225 | |
243 | |
244 | |
245 </help> | |
246 </tool> |