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comparison augustus.xml @ 2:a77a4e9921e0 draft

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author bgruening
date Wed, 06 May 2015 14:31:02 -0400
parents e2b822d7408f
children f5075dee9d6b
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1:e2b822d7408f 2:a77a4e9921e0
1 <tool id="augustus" name="Augustus" version="0.3.1"> 1 <tool id="augustus" name="Augustus" version="0.3.1">
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="2.7">augustus</requirement>
6 <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>
7 </requirements> 6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <regex match="Error:" />
11 <regex match="Exception:" />
12 </stdio>
8 <command> 13 <command>
14 <![CDATA[
9 ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config 15 ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
10 ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed 16 ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed
11 ## 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 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
12 18
13 augustus 19 augustus
14 --strand=$strand 20 --strand=$strand
15 $noInFrameStop 21 $noInFrameStop
16 $gff 22 $gff
17 23
18 #if 'protein' in str($outputs).split(','): 24 #if 'protein' in str($outputs).split(','):
19 --protein=on 25 --protein=on
20 #else: 26 #else:
21 --protein=off 27 --protein=off
22 #end if 28 #end if
24 #if 'codingseq' in str($outputs).split(','): 30 #if 'codingseq' in str($outputs).split(','):
25 --codingseq=on 31 --codingseq=on
26 #else: 32 #else:
27 --codingseq=off 33 --codingseq=off
28 #end if 34 #end if
29 35
30 #if 'introns' in str($outputs).split(','): 36 #if 'introns' in str($outputs).split(','):
31 --introns=on 37 --introns=on
32 #else: 38 #else:
33 --introns=off 39 --introns=off
34 #end if 40 #end if
56 $mea 62 $mea
57 $utr 63 $utr
58 --genemodel=$genemodel 64 --genemodel=$genemodel
59 --species=$organism 65 --species=$organism
60 ##--outfile=$output 66 ##--outfile=$output
61 | tee $output 67 | tee $output
62 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','): 68 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
63 | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py 69 | python $__tool_directory__/extract_features.py
64 #if 'protein' in str($outputs).split(','): 70 #if 'protein' in str($outputs).split(','):
65 --protein $protein_output 71 --protein $protein_output
66 #end if 72 #end if
67 #if 'codingseq' in str($outputs).split(','): 73 #if 'codingseq' in str($outputs).split(','):
68 --codingseq $codingseq_output 74 --codingseq $codingseq_output
69 #end if 75 #end if
70 #end if 76 #end if
77 ]]>
71 </command> 78 </command>
72 <inputs> 79 <inputs>
73 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> 80 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
74 <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" /> 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" />
75 <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" /> 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" />
134 <option value="pneumocystis">Pneumocystis jirovecii</option> 141 <option value="pneumocystis">Pneumocystis jirovecii</option>
135 <option value="chicken">Gallus gallus domesticus (chicken)</option> 142 <option value="chicken">Gallus gallus domesticus (chicken)</option>
136 <option value="cacao">Theobroma cacao (cacao)</option> 143 <option value="cacao">Theobroma cacao (cacao)</option>
137 <option value="heliconius_melpomene1">Heliconius melpomene</option> 144 <option value="heliconius_melpomene1">Heliconius melpomene</option>
138 <option value="xenoturbella">Xenoturbella</option> 145 <option value="xenoturbella">Xenoturbella</option>
139 </param> 146 </param>
140 147
141 <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand."> 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.">
142 <option value="both">both</option> 149 <option value="both">both</option>
143 <option value="forward">forward</option> 150 <option value="forward">forward</option>
144 <option value="backward">backward</option> 151 <option value="backward">backward</option>
145 </param> 152 </param>
146 153
147 <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."> 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.">
148 <option value="complete">complete</option> 155 <option value="complete">complete</option>
149 <option value="partial">partial</option> 156 <option value="partial">partial</option>
150 <option value="intronless">intronless</option> 157 <option value="intronless">intronless</option>
211 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> 218 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
212 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> 219 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
213 </test> 220 </test>
214 </tests> 221 </tests>
215 <help> 222 <help>
223 <![CDATA[
216 224
217 **What it does** 225 **What it does**
218 226
219 AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. 227 AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
220 It can be used as an ab initio program, which means it bases its prediction purely on the 228 It can be used as an ab initio program, which means it bases its prediction purely on the
269 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6"; 277 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
270 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6"; 278 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
271 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; 279 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
272 280
273 281
274 **References** 282 ]]>
275
276 Mario Stanke and Stephan Waack (2003)
277 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
278 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
279
280
281 </help> 283 </help>
284 <citations>
285 <citation type="doi">10.1093/bioinformatics/btg1080</citation>
286 </citations>
282 </tool> 287 </tool>