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comparison augustus.xml @ 1:e2b822d7408f draft

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Uploaded
author bgruening
date Thu, 05 Dec 2013 09:44:17 -0500
parents af307d3285c5
children a77a4e9921e0
comparison
equal deleted inserted replaced
0:af307d3285c5 1:e2b822d7408f
1 <tool id="augustus" name="Augustus" version="0.3"> 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 <requirements> 4 <requirements>
4 <requirement type="package" version="2.7">augustus</requirement> 5 <requirement type="package" version="2.7">augustus</requirement>
5 <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement> 6 <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>
6 </requirements> 7 </requirements>
7 <command> 8 <command>
11 12
12 augustus 13 augustus
13 --strand=$strand 14 --strand=$strand
14 $noInFrameStop 15 $noInFrameStop
15 $gff 16 $gff
16 $protein 17
17 $introns 18 #if 'protein' in str($outputs).split(','):
18 $start 19 --protein=on
19 $stop 20 #else:
20 $cds 21 --protein=off
21 $codingseq 22 #end if
23
24 #if 'codingseq' in str($outputs).split(','):
25 --codingseq=on
26 #else:
27 --codingseq=off
28 #end if
29
30 #if 'introns' in str($outputs).split(','):
31 --introns=on
32 #else:
33 --introns=off
34 #end if
35
36 #if 'start' in str($outputs).split(','):
37 --start=on
38 #else:
39 --stop=off
40 #end if
41
42 #if 'stop' in str($outputs).split(','):
43 --stop=on
44 #else:
45 --stop=off
46 #end if
47
48 #if 'cds' in str($outputs).split(','):
49 --cds=on
50 #else:
51 --cds=off
52 #end if
53
22 $singlestrand 54 $singlestrand
23 $input_genome 55 $input_genome
24 $mea 56 $mea
25 $utr 57 $utr
26 --genemodel=$genemodel 58 --genemodel=$genemodel
27 --species=$organism 59 --species=$organism
28 ##--outfile=$output 60 ##--outfile=$output
29 | tee $output 61 | tee $output
30 #if $protein or $codingseq: 62 #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
31 | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py 63 | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py
32 #if $protein: 64 #if 'protein' in str($outputs).split(','):
33 --protein $protein_output 65 --protein $protein_output
34 #end if 66 #end if
35 #if $codingseq: 67 #if 'codingseq' in str($outputs).split(','):
36 --codingseq $codingseq_output 68 --codingseq $codingseq_output
37 #end if 69 #end if
38 #end if 70 #end if
39 </command> 71 </command>
40 <inputs> 72 <inputs>
119 <option value="atleastone">atleastone</option> 151 <option value="atleastone">atleastone</option>
120 <option value="exactlyone">exactlyone</option> 152 <option value="exactlyone">exactlyone</option>
121 <option value="bacterium">bacterium (beta version)</option> 153 <option value="bacterium">bacterium (beta version)</option>
122 </param> 154 </param>
123 155
124 <param name="protein" type="boolean" label="Output predicted protein sequences (--protein)" truevalue="--protein=on" falsevalue="--protein=off" checked="true" /> 156
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" /> 157 <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
158
159 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
160 <option value="protein" selected="True">predicted protein sequences (--protein)</option>
161 <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
162 <option value="introns">predicted intron sequences (--introns)</option>
163 <option value="start">predicted start codons (--start)</option>
164 <option value="stop">predicted stop codons (--stop)</option>
165 <option value="cds" selected="true">CDS region (--cds)</option>
166
167 <validator type="no_options" message="Please select at least one output file." />
168 </param>
169
131 170
132 </inputs> 171 </inputs>
133 <outputs> 172 <outputs>
134 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF"> 173 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
135 <change_format> 174 <change_format>
136 <when input="gff" value="--gff3=on" format="gff" /> 175 <when input="gff" value="--gff3=on" format="gff" />
137 </change_format> 176 </change_format>
138 </data> 177 </data>
139 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence"> 178 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
140 <filter>protein == True</filter> 179 <filter>'protein' in outputs</filter>
141 </data> 180 </data>
142 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence"> 181 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
143 <filter>codingseq == True</filter> 182 <filter>'codingseq' in outputs</filter>
144 </data> 183 </data>
145 </outputs> 184 </outputs>
146 <tests> 185 <tests>
147 <test> 186 <test>
148 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 187 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
165 <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/> 204 <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>
166 </test> 205 </test>
167 <test> 206 <test>
168 <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> 207 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
169 <param name="organism" value="human" /> 208 <param name="organism" value="human" />
170 <param name="protein" value="--protein=on" /> 209 <param name="outputs" value="protein,codingseq,introns,cds" />
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"/> 210 <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" /> 211 <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" /> 212 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
177 </test> 213 </test>
178 </tests> 214 </tests>