Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

comparison NmrBucketing_wrapper.R @ 4:d61f6ceef5d6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
author lecorguille
date Tue, 22 Nov 2016 05:22:03 -0500
parents a99a6026c972
children
comparison
equal deleted inserted replaced
3:58679e85745f 4:d61f6ceef5d6
76 76
77 ## Parameters Loading 77 ## Parameters Loading
78 ##------------------- 78 ##-------------------
79 # Inputs 79 # Inputs
80 if (!is.null(argLs[["zipfile"]])){ 80 if (!is.null(argLs[["zipfile"]])){
81 fileType="zip"
81 zipfile= argLs[["zipfile"]] 82 zipfile= argLs[["zipfile"]]
82 directory=unzip(zipfile, list=F) 83 directory=unzip(zipfile, list=F)
83 directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") 84 directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
84 } else if (!is.null(argLs[["library"]])){ 85 } else if (!is.null(argLs[["library"]])){
86 fileType="zip"
85 directory=argLs[["library"]] 87 directory=argLs[["library"]]
86 if(!file.exists(directory)){ 88 if(!file.exists(directory)){
87 error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") 89 error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.")
88 print(error_message) 90 print(error_message)
89 stop(error_message) 91 stop(error_message)
90 } 92 }
93 } else if (!is.null(argLs[["tsvfile"]])){
94 fileType="tsv"
95 directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t")
91 } 96 }
92 97
93 leftBorder <- argLs[["left_border"]] 98 leftBorder <- argLs[["left_border"]]
94 rightBorder <- argLs[["right_border"]] 99 rightBorder <- argLs[["right_border"]]
95 bucketSize <- argLs[["bucket_width"]] 100 bucketSize <- argLs[["bucket_width"]]
109 # Outputs 114 # Outputs
110 nomGraphe <- argLs[["graphOut"]] 115 nomGraphe <- argLs[["graphOut"]]
111 dataMatrixOut <- argLs[["dataMatrixOut"]] 116 dataMatrixOut <- argLs[["dataMatrixOut"]]
112 sampleMetadataOut <- argLs[["sampleOut"]] 117 sampleMetadataOut <- argLs[["sampleOut"]]
113 variableMetadataOut <- argLs[["variableOut"]] 118 variableMetadataOut <- argLs[["variableOut"]]
114 log <- argLs[["logOut"]] 119 logFile <- argLs[["logOut"]]
115 120
116 ## Checking arguments 121 ## Checking arguments
117 ##------------------- 122 ##-------------------
118 error.stock <- "\n" 123 error.stock <- "\n"
119 124
121 stop(error.stock) 126 stop(error.stock)
122 127
123 128
124 ## Computation 129 ## Computation
125 ##------------ 130 ##------------
126 outputs <- NmrBucketing(directory,leftBorder,rightBorder,bucketSize,exclusionZones,exclusionZonesBorders,graphique,nomGraphe,log) 131 outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize,
132 exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe,
133 savLog.txtC=logFile)
127 data_bucket <- outputs[[1]] 134 data_bucket <- outputs[[1]]
128 data_sample <- outputs[[2]] 135 data_sample <- outputs[[2]]
129 data_variable <- outputs[[3]] 136 data_variable <- outputs[[3]]
130 137
131 ## Saving 138 ## Saving