Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.R @ 8:fa6aa0d5a27c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Mon, 09 May 2016 12:55:26 -0400
parents b83a4002aab1
children 328a1e3b5261
comparison
equal deleted inserted replaced
7:b83a4002aab1 8:fa6aa0d5a27c
39 procodingseq_file = GalaxyInputFile(required=TRUE), 39 procodingseq_file = GalaxyInputFile(required=TRUE),
40 rpkmCutoff = GalaxyNumericParam(required=TRUE), 40 rpkmCutoff = GalaxyNumericParam(required=TRUE),
41 ids_file = GalaxyInputFile(required=TRUE), 41 ids_file = GalaxyInputFile(required=TRUE),
42 outputFile = GalaxyOutput("FASTA","fasta")) 42 outputFile = GalaxyOutput("FASTA","fasta"))
43 { 43 {
44 file.symlink(exon_anno_file, paste(dirname(exon_anno_file), "exon_anno.RData", sep="/")) 44 file.symlink(exon_anno_file, "exon_anno.RData")
45 file.symlink(proteinseq_file, paste(dirname(exon_anno_file), "proseq.RData", sep="/")) 45 file.symlink(proteinseq_file, "proseq.RData")
46 file.symlink(procodingseq_file, paste(dirname(exon_anno_file), "procodingseq.RData", sep="/")) 46 file.symlink(procodingseq_file, "procodingseq.RData")
47 file.symlink(ids_file, paste(dirname(exon_anno_file), "ids.RData", sep="/")) 47 file.symlink(ids_file, "ids.RData")
48 48
49 bamLink = paste(dirname(bam_file), "input.bam", sep="/") 49 bamLink = "input.bam"
50 file.symlink(bam_file, bamLink) 50 file.symlink(bam_file, bamLink)
51 file.symlink(bai_file, paste(bamLink, ".bai", sep="")) 51 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
52 52
53 suppressPackageStartupMessages(library(customProDB)) 53 suppressPackageStartupMessages(library(customProDB))
54 54