Mercurial > repos > jjkoehorst > sapp
comparison sappDocker/priam.xml @ 31:957156367442 draft
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| author | jjkoehorst |
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| date | Wed, 29 Jun 2016 01:36:58 -0400 |
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| 30:0a947cb25a3d | 31:957156367442 |
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| 1 <tool id="DPriam" name="PRIAM EC detection" version="1.0.0"> | |
| 2 <description/> | |
| 3 <requirements> | |
| 4 <container type="docker">jjkoehorst/sappdocker:PRIAM</container> | |
| 5 </requirements> | |
| 6 <command interpreter="docker">java -jar /priam/target/priam-0.0.1-SNAPSHOT-jar-with-dependencies.jar | |
| 7 '-input' '$input' -format TURTLE -output '$output' | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param format="ttl" label="ttl genome file" name="input" type="data"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="ttl" label="PRIAM: ${input.name}" name="output"/> | |
| 14 </outputs> | |
| 15 <help>EC detection using PRIAM. An RDF file with protein prediction is | |
| 16 required. Either from Genbank/EMBL or from Prodigal gene prediction | |
| 17 module. | |
| 18 </help> | |
| 19 <citations> | |
| 20 <citation type="bibtex">@article{Claudel-Renard2003, | |
| 21 abstract = {The | |
| 22 advent of fully sequenced genomes opens the ground for the | |
| 23 reconstruction of metabolic pathways on the basis of the | |
| 24 identification of enzyme-coding genes. Here we describe PRIAM, a | |
| 25 method for automated enzyme detection in a fully sequenced genome, | |
| 26 based on the classification of enzymes in the ENZYME database. PRIAM | |
| 27 relies on sets of position-specific scoring matrices ( profiles') | |
| 28 automatically tailored for each ENZYME entry. Automatically generated | |
| 29 logical rules define which of these profiles is required in order to | |
| 30 infer the presence of the corresponding enzyme in an organism. As an | |
| 31 example, PRIAM was applied to identify potential metabolic pathways | |
| 32 from the complete genome of the nitrogen-fixing bacterium | |
| 33 Sinorhizobium meliloti. The results of this automated method were | |
| 34 compared with the original genome annotation and visualised on KEGG | |
| 35 graphs in order to facilitate the interpretation of metabolic | |
| 36 pathways and to highlight potentially missing enzymes.}, | |
| 37 author = | |
| 38 {Claudel-Renard, C.}, | |
| 39 doi = {10.1093/nar/gkg847}, | |
| 40 issn = {1362-4962}, | |
| 41 journal = {Nucleic Acids Research}, | |
| 42 month = nov, | |
| 43 number = {22}, | |
| 44 pages = | |
| 45 {6633--6639}, | |
| 46 title = {{Enzyme-specific profiles for genome | |
| 47 annotation: PRIAM}}, | |
| 48 url = | |
| 49 {http://nar.oxfordjournals.org/content/31/22/6633.abstract?etoc}, | |
| 50 volume = {31}, | |
| 51 year = {2003} | |
| 52 } | |
| 53 </citation> | |
| 54 </citations> | |
| 55 </tool> |