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1 <tool id="DPriam" name="PRIAM EC 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:PRIAM</container>
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5 </requirements>
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6 <command interpreter="docker">java -jar /priam/target/priam-0.0.1-SNAPSHOT-jar-with-dependencies.jar
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7 '-input' '$input' -format TURTLE -output '$output'
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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 </inputs>
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12 <outputs>
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13 <data format="ttl" label="PRIAM: ${input.name}" name="output"/>
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14 </outputs>
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15 <help>EC detection using PRIAM. An RDF file with protein prediction is
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16 required. Either from Genbank/EMBL or from Prodigal gene prediction
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17 module.
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18 </help>
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19 <citations>
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20 <citation type="bibtex">@article{Claudel-Renard2003,
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21 abstract = {The
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22 advent of fully sequenced genomes opens the ground for the
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23 reconstruction of metabolic pathways on the basis of the
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24 identification of enzyme-coding genes. Here we describe PRIAM, a
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25 method for automated enzyme detection in a fully sequenced genome,
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26 based on the classification of enzymes in the ENZYME database. PRIAM
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27 relies on sets of position-specific scoring matrices ( profiles')
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28 automatically tailored for each ENZYME entry. Automatically generated
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29 logical rules define which of these profiles is required in order to
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30 infer the presence of the corresponding enzyme in an organism. As an
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31 example, PRIAM was applied to identify potential metabolic pathways
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32 from the complete genome of the nitrogen-fixing bacterium
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33 Sinorhizobium meliloti. The results of this automated method were
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34 compared with the original genome annotation and visualised on KEGG
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35 graphs in order to facilitate the interpretation of metabolic
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36 pathways and to highlight potentially missing enzymes.},
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37 author =
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38 {Claudel-Renard, C.},
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39 doi = {10.1093/nar/gkg847},
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40 issn = {1362-4962},
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41 journal = {Nucleic Acids Research},
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42 month = nov,
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43 number = {22},
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44 pages =
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45 {6633--6639},
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46 title = {{Enzyme-specific profiles for genome
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47 annotation: PRIAM}},
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48 url =
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49 {http://nar.oxfordjournals.org/content/31/22/6633.abstract?etoc},
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50 volume = {31},
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51 year = {2003}
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52 }
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53 </citation>
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54 </citations>
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55 </tool> |
