annotate priam.xml @ 35:fa736576c7ed draft

planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty

<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>