Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

comparison data_manager/customProDB_annotation.R @ 4:b42974daa659 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 Thu, 28 Jan 2016 18:46:50 -0500
parents af0a098e15bd
children a0ca66b32792
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3:af0a098e15bd 4:b42974daa659
67 cat(paste("Preparing Refseq annotation files\n")) 67 cat(paste("Preparing Refseq annotation files\n"))
68 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory) 68 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory)
69 69
70 outputPath = paste(dbkey, "/customProDB", sep="") 70 outputPath = paste(dbkey, "/customProDB", sep="")
71 output = list(data_tables = list()) 71 output = list(data_tables = list())
72 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey) 72 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey, value=dbkey)
73 write(toJSON(output), file=outputFile) 73 write(toJSON(output), file=outputFile)
74 } 74 }
75 75
76 76
77 params <- list() 77 params <- list()