Mercurial > repos > jjkoehorst > sapp
comparison sappDocker/signalp.xml @ 31:957156367442 draft
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| author | jjkoehorst |
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| date | Wed, 29 Jun 2016 01:36:58 -0400 |
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| 30:0a947cb25a3d | 31:957156367442 |
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| 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> |