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author jjkoehorst
date Mon, 04 Jul 2016 10:53:52 -0400
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children
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1 <tool id="DSignalp" name="Signal peptide detection" version="1.0.0">
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2 <description/>
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3 <requirements>
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4 <container type="docker">jjkoehorst/sappdocker:SIGNALP</container>
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5 </requirements>
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6 <command interpreter="docker">java -jar /signalp/signalp-0.0.1-SNAPSHOT-jar-with-dependencies.jar
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7 '-signaltype' '$runtype' -input $input -output $output -format TURTLE
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8 </command>
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9 <inputs>
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10 <param format="ttl" label="ttl genome file" name="input" type="data"/>
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11 <param label="Gram+/- or Eukaryotes" name="runtype" type="select">
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12 <option value="gram+">Gram+ Bacteria</option>
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13 <option value="gram-">Gram- Bacteria</option>
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14 <option value="euk">Eukaryotes</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="ttl" label="signalP: ${input.name}" name="output"/>
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19 </outputs>
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20 <help>Be aware that this can only be used for academic users; other
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21 users are
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22 requested to contact CBS Software Package Manager at
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23 software@cbs.dtu.dk.
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24 We are investigating alternative prediction
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25 applications, please contact
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26 us if you are aware of such method.
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27 </help>
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28 <citations>
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29 <citation type="bibtex">@article{Petersen2011,
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30 author = {Petersen,
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31 Thomas Nordahl and Brunak, S\o ren and von Heijne,
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32 Gunnar and Nielsen,
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33 Henrik},
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34 doi = {10.1038/nmeth.1701},
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35 issn = {1548-7105},
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36 journal =
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37 {Nature methods},
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38 keywords = {Algorithms,Cell Membrane,Cell Membrane:
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39 metabolism,Computational
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40 Biology,Protein Sorting Signals,Software},
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41 mendeley-groups = {Dump/VAPP Paper},
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42 month = jan,
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43 number = {10},
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44 pages =
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45 {785--6},
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46 pmid = {21959131},
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47 publisher = {Nature Publishing Group},
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48 title = {{SignalP 4.0: discriminating signal peptides from
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49 transmembrane
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50 regions.}},
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51 url =
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52 {http://www.ncbi.nlm.nih.gov/pubmed/21959131},
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53 volume = {8},
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54 year =
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55 {2011}
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56 }
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57 </citation>
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58 </citations>
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59 </tool>