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comparison signalp.xml @ 35:fa736576c7ed draft

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planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
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34:f2cbf1230026 35:fa736576c7ed
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/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>