diff interproscan.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty

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+<tool id="DInterproscan" name="Interproscan" version="1.0.0">
+	<description>Interproscan annotation for SAPP</description>
+	<requirements>
+		<container type="docker">jjkoehorst/sappdocker:INTERPROSCAN</container>
+	</requirements>
+	<command interpreter="docker">java -jar /interproscan/interproscanRDF-0.0.1-SNAPSHOT-jar-with-dependencies.jar
+		'-input' '$input' '-format' 'TURTLE'
+		'-applications' '$appl'
+		'-output'
+		'$outfile' -v '$version' '$disable'
+	</command>
+	<inputs>
+		<param format="ttl" label="genome rdf file with orf prediction" name="input" type="data"/>
+		<param display="checkboxes" help="Select your programm." label="Applications to run" multiple="True" name="appl" type="select">
+			<option selected="true" value="TIGRFAM">TIGRFAM: protein families
+				based on Hidden Markov Models or HMMs
+			</option>
+			<option selected="false" value="PIRSF">PIRSF: non-overlapping
+				clustering of UniProtKB sequences into a hierarchical order
+				(evolutionary relationships)
+			</option>
+			<option selected="true" value="ProDom">ProDom: set of protein domain
+				families generated from the UniProtKB
+			</option>
+			<option selected="true" value="SMART">SMART: identification and
+				analysis of domain architectures based on Hidden Markov Models or
+				HMMs
+			</option>
+			<option selected="false" value="PrositeProfiles">PROSITE Profiles:
+				protein domains, families and functional sites as well as associated
+				profiles to identify them
+			</option>
+			<option selected="true" value="PrositePatterns">PROSITE Pattern:
+				protein domains, families and functional sites as well as associated
+				patterns to identify them
+			</option>
+			<option selected="false" value="HAMAP">HAMAP: High-quality Automated
+				Annotation of Microbial Proteomes
+			</option>
+			<option selected="true" value="PfamA">PfamA: protein families, each
+				represented by multiple sequence alignments and hidden Markov models
+			</option>
+			<option selected="true" value="PRINTS">PRINTS: group of conserved
+				motifs (fingerprints) used to characterise a protein family
+			</option>
+			<option selected="true" value="SuperFamily">SUPERFAMILY: database of
+				structural and functional annotation
+			</option>
+			<option selected="true" value="Coils">Coils: Prediction of Coiled
+				Coil Regions in Proteins
+			</option>
+			<option selected="true" value="Gene3d">Gene3d: Structural assignment
+				for whole genes and genomes using the CATH domain structure database
+			</option>
+		</param>
+		<param label="Version selection" name="version" type="select">
+			<option value="interproscan-5.17-56.0">interproscan-5.17-56.0</option>
+		</param>
+		<param checked="false" falsevalue="-disableprecalc" help="You need to setup your own lookup server as the EBI version can differ. Look at interproscan configuration file for more info" label="Perform lookup of InterPro at defined server address" name="disable" truevalue="" type="boolean"/>
+	</inputs>
+	<outputs>
+		<data format="ttl" label="IPR: ${input.name}" name="outfile"/>
+	</outputs>
+	<help>Interproscan annotation suite. Select your RDF genome with
+		protein annotation.
+		This can be either from a converted GenBank/EMBL
+		file or from a
+		Prodigal prediction.
+		The output will be an RDF file with
+		protein domain annotation from
+		InterPro.
+	</help>
+	<citations>
+		<citation type="bibtex">@article{Mitchell26112014,
+			author = {Mitchell,
+			Alex and Chang, Hsin-Yu and Daugherty, Louise and
+			Fraser, Matthew and
+			Hunter, Sarah and Lopez, Rodrigo and McAnulla,
+			Craig and McMenamin,
+			Conor and Nuka, Gift and Pesseat, Sebastien and
+			Sangrador-Vegas, Amaia
+			and Scheremetjew, Maxim and Rato, Claudia and
+			Yong, Siew-Yit and
+			Bateman, Alex and Punta, Marco and Attwood, Teresa
+			K. and Sigrist,
+			Christian J.A. and Redaschi, Nicole and Rivoire,
+			Catherine and
+			Xenarios, Ioannis and Kahn, Daniel and Guyot, Dominique
+			and Bork, Peer
+			and Letunic, Ivica and Gough, Julian and Oates, Matt
+			and Haft, Daniel
+			and Huang, Hongzhan and Natale, Darren A. and Wu,
+			Cathy H. and Orengo,
+			Christine and Sillitoe, Ian and Mi, Huaiyu and
+			Thomas, Paul D. and
+			Finn, Robert D.},
+			title = {The InterPro protein families database: the
+			classification
+			resource after 15 years},
+			year = {2014},
+			doi =
+			{10.1093/nar/gku1243},
+			abstract ={The InterPro database
+			(http://www.ebi.ac.uk/interpro/) is a freely
+			available resource that
+			can be used to classify sequences into
+			protein families and to predict
+			the presence of important domains and
+			sites. Central to the InterPro
+			database are predictive models, known
+			as signatures, from a range of
+			different protein family databases
+			that have different biological
+			focuses and use different
+			methodological approaches to classify
+			protein families and domains.
+			InterPro integrates these signatures,
+			capitalizing on the respective
+			strengths of the individual databases,
+			to produce a powerful protein
+			classification resource. Here, we report
+			on the status of InterPro as
+			it enters its 15th year of operation, and
+			give an overview of new
+			developments with the database and its
+			associated Web interfaces and
+			software. In particular, the new domain
+			architecture search tool is
+			described and the process of mapping of
+			Gene Ontology terms to
+			InterPro is outlined. We also discuss the
+			challenges faced by the
+			resource given the explosive growth in
+			sequence data in recent years.
+			InterPro (version 48.0) contains 36 766
+			member database signatures
+			integrated into 26 238 InterPro entries, an
+			increase of over 3993
+			entries (5081 signatures), since 2012.},
+			URL =
+			{http://nar.oxfordjournals.org/content/early/2014/11/26/nar.gku1243.abstract},
+			eprint =
+			{http://nar.oxfordjournals.org/content/early/2014/11/26/nar.gku1243.full.pdf+html},
+			journal = {Nucleic Acids Research}
+			}
+		</citation>
+	</citations>
+</tool>
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