Mercurial > repos > sblanck > mpagenomics
comparison preprocess.R @ 4:3fcbb8030fcc draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author | sblanck |
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date | Mon, 12 Apr 2021 14:47:09 +0000 |
parents | 4d539083cf7f |
children |
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3:94fc6ed13946 | 4:3fcbb8030fcc |
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1 #!/usr/bin/env Rscript | 1 #!/usr/bin/env Rscript |
2 # setup R error handling to go to stderr | 2 # setup R error handling to go to stderr |
3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | 3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
4 | 4 |
5 # we need that to not crash galaxy with an UTF8 error on German LC settings. | 5 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | 6 #loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
7 | 7 |
8 library("optparse") | 8 library("optparse") |
9 | 9 |
10 ##### Read options | 10 ##### Read options |
11 option_list=list( | 11 option_list=list( |
22 make_option("--inputacs",type="character",default=NULL, dest="inputacs"), | 22 make_option("--inputacs",type="character",default=NULL, dest="inputacs"), |
23 make_option("--tumorcsv",type="character",default=NULL, dest="tumorcsv"), | 23 make_option("--tumorcsv",type="character",default=NULL, dest="tumorcsv"), |
24 make_option("--settingsType",type="character",default=NULL, dest="settingsType"), | 24 make_option("--settingsType",type="character",default=NULL, dest="settingsType"), |
25 make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"), | 25 make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"), |
26 make_option("--zipfigures",type="character",default=NULL, dest="zipfigures"), | 26 make_option("--zipfigures",type="character",default=NULL, dest="zipfigures"), |
27 make_option("--zipresults",type="character",default=NULL, dest="zipresults"), | |
27 make_option("--outputlog",type="character",default=NULL, dest="outputlog"), | 28 make_option("--outputlog",type="character",default=NULL, dest="outputlog"), |
28 make_option("--log",type="character",default=NULL, dest="log"), | 29 make_option("--log",type="character",default=NULL, dest="log"), |
29 make_option("--user_id",type="character",default=NULL, dest="user_id"), | 30 make_option("--user_id",type="character",default=NULL, dest="user_id"), |
30 make_option("--input",type="character",default=NULL, dest="input") | 31 make_option("--input",type="character",default=NULL, dest="input") |
31 ); | 32 ); |
53 inputACS=opt$inputacs | 54 inputACS=opt$inputacs |
54 tumorcsv=opt$tumorcsv | 55 tumorcsv=opt$tumorcsv |
55 settingsType=opt$settingsType | 56 settingsType=opt$settingsType |
56 outputGraph=opt$outputgraph | 57 outputGraph=opt$outputgraph |
57 zipfigures=opt$zipfigures | 58 zipfigures=opt$zipfigures |
59 zipresults=opt$zipresults | |
58 outputlog=opt$outputlog | 60 outputlog=opt$outputlog |
59 log=opt$log | 61 log=opt$log |
60 userId=opt$user_id | 62 userId=opt$user_id |
61 | 63 |
62 destinationPath=file.path(newFilePath, userId, dataSetName) | 64 destinationPath=file.path(newFilePath, userId, dataSetName) |
127 tumor=tumorcsv | 129 tumor=tumorcsv |
128 outputgraph=type.convert(outputGraph) | 130 outputgraph=type.convert(outputGraph) |
129 | 131 |
130 | 132 |
131 library(MPAgenomics) | 133 library(MPAgenomics) |
134 library(R.utils) | |
135 library(aroma.affymetrix) | |
136 | |
132 setwd(workdir) | 137 setwd(workdir) |
133 | 138 |
134 if (outputlog){ | 139 if (outputlog){ |
135 sinklog <- file(log, open = "wt") | 140 sinklog <- file(log, open = "wt") |
136 sink(sinklog ,type = "output") | 141 sink(sinklog ,type = "output") |
141 { | 146 { |
142 signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) | 147 signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) |
143 } else { | 148 } else { |
144 signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, normalTumorArray=tumor, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) | 149 signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, normalTumorArray=tumor, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) |
145 } | 150 } |
151 setwd(mpagenomicsDir) | |
152 library(zip) | |
153 zipr(zipresults,files=".") | |
146 setwd(abs_fig_dir) | 154 setwd(abs_fig_dir) |
155 #abs_fig_dir | |
147 files2zip <- dir(abs_fig_dir) | 156 files2zip <- dir(abs_fig_dir) |
148 zip(zipfile = "figures.zip", files = files2zip) | 157 zipr(zipfigures, files = files2zip) |
149 file.rename("figures.zip",zipfigures) | 158 |
150 summarydf=data.frame(celFileNameList,rep(dataSetName,length(celFileNameList)),rep(chipType,length(celFileNameList))) | 159 summarydf=data.frame(celFileNameList,rep(dataSetName,length(celFileNameList)),rep(chipType,length(celFileNameList))) |
151 write.table(summarydf,file=summary,quote=FALSE,row.names=FALSE,col.names=FALSE,sep="\t") | 160 write.table(summarydf,file=summary,quote=FALSE,row.names=FALSE,col.names=FALSE,sep="\t") |
161 | |
162 if (dir.exists(mpagenomicsDir)) { | |
163 system(paste0("rm -r ", mpagenomicsDir)) | |
164 dir.create(mpagenomicsDir, showWarnings = TRUE, recursive = TRUE) | |
165 } | |
166 | |
167 if (dir.exists(dataDir)) { | |
168 system(paste0("rm -r ", dataDir)) | |
169 dir.create(dataDir, showWarnings = TRUE, recursive = TRUE) | |
170 } | |
152 | 171 |
153 if (outputlog){ | 172 if (outputlog){ |
154 sink(type="output") | 173 sink(type="output") |
155 sink(type="message") | 174 sink(type="message") |
156 close(sinklog) | 175 close(sinklog) |