diff priam.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty

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+<tool id="DPriam" name="PRIAM EC detection" version="1.0.0">
+	<description/>
+	<requirements>
+		<container type="docker">jjkoehorst/sappdocker:PRIAM</container>
+	</requirements>
+	<command interpreter="docker">java -jar /priam/priam-0.0.1-SNAPSHOT-jar-with-dependencies.jar
+		'-input' '$input' -format TURTLE -output '$output'
+	</command>
+	<inputs>
+		<param format="ttl" label="ttl genome file" name="input" type="data"/>
+	</inputs>
+	<outputs>
+		<data format="ttl" label="PRIAM: ${input.name}" name="output"/>
+	</outputs>
+	<help>EC detection using PRIAM. An RDF file with protein prediction is
+		required. Either from Genbank/EMBL or from Prodigal gene prediction
+		module.
+	</help>
+	<citations>
+		<citation type="bibtex">@article{Claudel-Renard2003,
+			abstract = {The
+			advent of fully sequenced genomes opens the ground for the
+			reconstruction of metabolic pathways on the basis of the
+			identification of enzyme-coding genes. Here we describe PRIAM, a
+			method for automated enzyme detection in a fully sequenced genome,
+			based on the classification of enzymes in the ENZYME database. PRIAM
+			relies on sets of position-specific scoring matrices ( profiles')
+			automatically tailored for each ENZYME entry. Automatically generated
+			logical rules define which of these profiles is required in order to
+			infer the presence of the corresponding enzyme in an organism. As an
+			example, PRIAM was applied to identify potential metabolic pathways
+			from the complete genome of the nitrogen-fixing bacterium
+			Sinorhizobium meliloti. The results of this automated method were
+			compared with the original genome annotation and visualised on KEGG
+			graphs in order to facilitate the interpretation of metabolic
+			pathways and to highlight potentially missing enzymes.},
+			author =
+			{Claudel-Renard, C.},
+			doi = {10.1093/nar/gkg847},
+			issn = {1362-4962},
+			journal = {Nucleic Acids Research},
+			month = nov,
+			number = {22},
+			pages =
+			{6633--6639},
+			title = {{Enzyme-specific profiles for genome
+			annotation: PRIAM}},
+			url =
+			{http://nar.oxfordjournals.org/content/31/22/6633.abstract?etoc},
+			volume = {31},
+			year = {2003}
+			}
+		</citation>
+	</citations>
+</tool>
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