|
31
|
1 <tool id="DSignalp" name="Signal peptide detection" version="1.0.0">
|
|
|
2 <description/>
|
|
|
3 <requirements>
|
|
|
4 <container type="docker">jjkoehorst/sappdocker:SIGNALP</container>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="docker">java -jar /signalp/target/signalp-0.0.1-SNAPSHOT-jar-with-dependencies.jar
|
|
|
7 '-signaltype' '$runtype' -input $input -output $output -format TURTLE
|
|
|
8 </command>
|
|
|
9 <inputs>
|
|
|
10 <param format="ttl" label="ttl genome file" name="input" type="data"/>
|
|
|
11 <param label="Gram+/- or Eukaryotes" name="runtype" type="select">
|
|
|
12 <option value="gram+">Gram+ Bacteria</option>
|
|
|
13 <option value="gram-">Gram- Bacteria</option>
|
|
|
14 <option value="euk">Eukaryotes</option>
|
|
|
15 </param>
|
|
|
16 </inputs>
|
|
|
17 <outputs>
|
|
|
18 <data format="ttl" label="signalP: ${input.name}" name="output"/>
|
|
|
19 </outputs>
|
|
|
20 <help>Be aware that this can only be used for academic users; other
|
|
|
21 users are
|
|
|
22 requested to contact CBS Software Package Manager at
|
|
|
23 software@cbs.dtu.dk.
|
|
|
24 We are investigating alternative prediction
|
|
|
25 applications, please contact
|
|
|
26 us if you are aware of such method.
|
|
|
27 </help>
|
|
|
28 <citations>
|
|
|
29 <citation type="bibtex">@article{Petersen2011,
|
|
|
30 author = {Petersen,
|
|
|
31 Thomas Nordahl and Brunak, S\o ren and von Heijne,
|
|
|
32 Gunnar and Nielsen,
|
|
|
33 Henrik},
|
|
|
34 doi = {10.1038/nmeth.1701},
|
|
|
35 issn = {1548-7105},
|
|
|
36 journal =
|
|
|
37 {Nature methods},
|
|
|
38 keywords = {Algorithms,Cell Membrane,Cell Membrane:
|
|
|
39 metabolism,Computational
|
|
|
40 Biology,Protein Sorting Signals,Software},
|
|
|
41 mendeley-groups = {Dump/VAPP Paper},
|
|
|
42 month = jan,
|
|
|
43 number = {10},
|
|
|
44 pages =
|
|
|
45 {785--6},
|
|
|
46 pmid = {21959131},
|
|
|
47 publisher = {Nature Publishing Group},
|
|
|
48 title = {{SignalP 4.0: discriminating signal peptides from
|
|
|
49 transmembrane
|
|
|
50 regions.}},
|
|
|
51 url =
|
|
|
52 {http://www.ncbi.nlm.nih.gov/pubmed/21959131},
|
|
|
53 volume = {8},
|
|
|
54 year =
|
|
|
55 {2011}
|
|
|
56 }
|
|
|
57 </citation>
|
|
|
58 </citations>
|
|
|
59 </tool> |
