Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

comparison data_manager/customProDB_annotation.R @ 8:f4badf0bf23a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 08 Jun 2016 16:00:30 -0400
parents 7399b23db662
children 9fec6c7f46eb
comparison
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7:7399b23db662 8:f4badf0bf23a
89 89
90 cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n")) 90 cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n"))
91 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb') 91 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
92 92
93 cat(paste("Preparing Refseq annotation files\n")) 93 cat(paste("Preparing Refseq annotation files\n"))
94 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, cosmic=use_cosmic) 94 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, COSMIC=use_cosmic)
95 95
96 outputPath = paste(dbkey, "/customProDB", sep="") 96 outputPath = paste(dbkey, "/customProDB", sep="")
97 output = list(data_tables = list()) 97 output = list(data_tables = list())
98 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey, value=dbkey) 98 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey, value=dbkey)
99 write(toJSON(output), file=outputFile) 99 write(toJSON(output), file=outputFile)