Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.R @ 0:8ccfff69dd57 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
author galaxyp
date Tue, 14 Mar 2017 14:14:38 -0400
parents
children ad130eaa3a05
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8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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1 #!/usr/bin/env Rscript
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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3 initial.options <- commandArgs(trailingOnly = FALSE)
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
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8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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6 ## begin warning handler
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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7 withCallingHandlers({
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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8
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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9 library(methods) # Because Rscript does not always do this
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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10
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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11 options('useFancyQuotes' = FALSE)
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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12
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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13 suppressPackageStartupMessages(library("optparse"))
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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14 suppressPackageStartupMessages(library("RGalaxy"))
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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17 option_list <- list()
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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19 option_list$bam <- make_option('--bam', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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20 option_list$bai <- make_option('--bai', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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21 option_list$vcf <- make_option('--vcf', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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22 option_list$exon_anno <- make_option('--exon_anno', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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23 option_list$proteinseq <- make_option('--proteinseq', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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24 option_list$procodingseq <- make_option('--procodingseq', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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25 option_list$ids <- make_option('--ids', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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26 option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
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27 option_list$cosmic <- make_option('--cosmic', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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28 option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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29 option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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30 #option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
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31 #option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
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32 option_list$outputFile <- make_option('--outputFile', type='character')
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35 opt <- parse_args(OptionParser(option_list=option_list))
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38 customProDB <- function(
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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39 bam_file = GalaxyInputFile(required=TRUE),
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40 bai_file = GalaxyInputFile(required=TRUE),
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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41 vcf_file = GalaxyInputFile(required=TRUE),
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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42 exon_anno_file = GalaxyInputFile(required=TRUE),
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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43 proteinseq_file = GalaxyInputFile(required=TRUE),
8ccfff69dd57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
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44 procodingseq_file = GalaxyInputFile(required=TRUE),
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45 ids_file = GalaxyInputFile(required=TRUE),
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46 dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
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47 cosmic_file = GalaxyInputFile(required=FALSE),
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48 annotationFromHistory = GalaxyLogicalParam(required=FALSE),
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49 rpkmCutoff = GalaxyNumericParam(required=TRUE),
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50 #outputIndels = GalaxyLogicalParam(required=FALSE),
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51 #outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
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52 outputFile = GalaxyOutput("FASTA","fasta"))
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53 {
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54 file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
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55 file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
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56 file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
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57 file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
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58
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59 if (length(dbsnpinCoding_file) > 0)
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60 {
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61 file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
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62 labelrsid = T
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63 }
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64 else
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65 {
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66 labelrsid = F
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67 }
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68
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69 if (length(cosmic_file) > 0)
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70 {
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71 file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
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72 cosmic = T
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73 }
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74 else
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75 {
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76 cosmic = F
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77 }
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78
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79 bamLink = "input.bam"
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80 file.symlink(bam_file, bamLink)
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81 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
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82
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83 suppressPackageStartupMessages(library(customProDB))
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84
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85 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
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86 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
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87 nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
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88 }
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89
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90
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91 params <- list()
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92 for(param in names(opt))
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93 {
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94 if (!param == "help")
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95 params[param] <- opt[param]
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96 }
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97
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98 setClass("GalaxyRemoteError", contains="character")
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99 wrappedFunction <- function(f)
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100 {
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101 tryCatch(do.call(f, params),
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102 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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103 }
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104
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105
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106 suppressPackageStartupMessages(library(RGalaxy))
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107 do.call(customProDB, params)
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108
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109 ## end warning handler
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110 }, warning = function(w) {
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111 cat(paste("Warning:", conditionMessage(w), "\n"))
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112 invokeRestart("muffleWarning")
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113 })