Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

comparison data_manager/customProDB_annotation.R @ 2:20a1b026b798 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Tue, 26 Jan 2016 18:46:21 -0500
parents 663ee21a8609
children af0a098e15bd
comparison
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1:4c77cf5a2977 2:20a1b026b798
57 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb') 57 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
58 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory) 58 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory)
59 59
60 outputPath = paste("customProDB/", dbkey, sep="") 60 outputPath = paste("customProDB/", dbkey, sep="")
61 output = list(data_tables = list()) 61 output = list(data_tables = list())
62 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey, value=dbkey) 62 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey, value=dbkey, dbkey=dbkey)
63 write(toJSON(output), file=outputFile) 63 write(toJSON(output), file=outputFile)
64 } 64 }
65 65
66 66
67 params <- list() 67 params <- list()