view signalp.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty

<tool id="DSignalp" name="Signal peptide detection" version="1.0.0">
	<description/>
	<requirements>
		<container type="docker">jjkoehorst/sappdocker:SIGNALP</container>
	</requirements>
	<command interpreter="docker">java -jar /signalp/signalp-0.0.1-SNAPSHOT-jar-with-dependencies.jar
		'-signaltype' '$runtype' -input $input -output $output -format TURTLE
	</command>
	<inputs>
		<param format="ttl" label="ttl genome file" name="input" type="data"/>
		<param label="Gram+/- or Eukaryotes" name="runtype" type="select">
			<option value="gram+">Gram+ Bacteria</option>
			<option value="gram-">Gram- Bacteria</option>
			<option value="euk">Eukaryotes</option>
		</param>
	</inputs>
	<outputs>
		<data format="ttl" label="signalP: ${input.name}" name="output"/>
	</outputs>
	<help>Be aware that this can only be used for academic users; other
		users are
		requested to contact CBS Software Package Manager at
		[e-mail].
		We are investigating alternative prediction
		applications, please contact
		us if you are aware of such method.
	</help>
	<citations>
		<citation type="bibtex">@article{Petersen2011,
			author = {Petersen,
			Thomas Nordahl and Brunak, S\o ren and von Heijne,
			Gunnar and Nielsen,
			Henrik},
			doi = {10.1038/nmeth.1701},
			issn = {1548-7105},
			journal =
			{Nature methods},
			keywords = {Algorithms,Cell Membrane,Cell Membrane:
			metabolism,Computational
			Biology,Protein Sorting Signals,Software},
			mendeley-groups = {Dump/VAPP Paper},
			month = jan,
			number = {10},
			pages =
			{785--6},
			pmid = {21959131},
			publisher = {Nature Publishing Group},
			title = {{SignalP 4.0: discriminating signal peptides from
			transmembrane
			regions.}},
			url =
			{http://www.ncbi.nlm.nih.gov/pubmed/21959131},
			volume = {8},
			year =
			{2011}
			}
		</citation>
	</citations>
</tool>