Mercurial > repos > galaxyp > psm_to_sam

comparison PSM2SAM.R @ 3:ce09f1a1bbad draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Thu, 28 Jan 2016 18:40:54 -0500
parents 34f9e847dd4e
children cd69250e1150
comparison
equal deleted inserted replaced
2:e1bb35f6ca28 3:ce09f1a1bbad
30 30
31 31
32 32
33 PSMtab2SAM <- function( 33 PSMtab2SAM <- function(
34 passedPSM_file = GalaxyInputFile(required=TRUE), 34 passedPSM_file = GalaxyInputFile(required=TRUE),
35 exon_anno_file = GalaxyInputFile(), 35 exon_anno_file = GalaxyInputFile(required=TRUE),
36 proteinseq_file = GalaxyInputFile(), 36 proteinseq_file = GalaxyInputFile(required=TRUE),
37 procodingseq_file = GalaxyInputFile(), 37 procodingseq_file = GalaxyInputFile(required=TRUE),
38 header_file = GalaxyInputFile(), 38 header_file = GalaxyInputFile(required=TRUE),
39 XScolumn = GalaxyCharacterParam(required=TRUE), 39 XScolumn = GalaxyCharacterParam(required=TRUE),
40 OutputFile = GalaxyOutput("proSAM","sam")) 40 OutputFile = GalaxyOutput("proSAM","sam"))
41 { 41 {
42 if (length(exon_anno_file) == 0) { exon_anno_file = paste(script_parent_dir, "tool-data/exon_anno.RData", sep="/") }
43 if (length(proteinseq_file) == 0) { proteinseq_file = paste(script_parent_dir, "tool-data/proseq.RData", sep="/") }
44 if (length(procodingseq_file) == 0) { procodingseq_file = paste(script_parent_dir, "tool-data/procodingseq.RData", sep="/") }
45 if (length(header_file) == 0) { header_file = paste(script_parent_dir, "tool-data/header_refseq_hg19.txt", sep="/") }
46
47 if (!file.exists(header_file)) { gstop("failed to read header file") } 42 if (!file.exists(header_file)) { gstop("failed to read header file") }
48 if (file.exists(OutputFile)) 43 if (file.exists(OutputFile))
49 { 44 {
50 if (file.info(OutputFile)$size > 0) { gstop("output file already exists") } 45 if (file.info(OutputFile)$size > 0) { gstop("output file already exists") }
51 else 46 else
53 tryCatch( 48 tryCatch(
54 { 49 {
55 file.remove(OutputFile) 50 file.remove(OutputFile)
56 }, error=function(err) 51 }, error=function(err)
57 { 52 {
58 gstop("failed to read empty existing file") 53 gstop("failed to remove empty existing file")
59 }) 54 })
60 } 55 }
61 } 56 }
62 57
63 suppressPackageStartupMessages(library(GenomicRanges)) 58 suppressPackageStartupMessages(library(GenomicRanges))