Mercurial > repos > lecorguille > xcms_xcmsset

comparison xcms.r @ 27:8e46e9bd7c50 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5583baab62c0f17cabbfe93ba4f2522e8df9b36b
author lecorguille
date Thu, 30 Mar 2017 08:33:25 -0400
parents dc4d3e2b9968
children 5dba1c94fb94
comparison
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26:626d3db664ef 27:8e46e9bd7c50
99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL 99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
100 } 100 }
101 101
102 102
103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { 103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
104 rawFilePath = getRawfilePathFromArguments(listArguments) 104 if (!exists("singlefile")) singlefile=NULL
105 if (!exists("zipfile")) zipfile=NULL
106 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
105 zipfile = rawFilePath$zipfile 107 zipfile = rawFilePath$zipfile
106 singlefile = rawFilePath$singlefile 108 singlefile = rawFilePath$singlefile
107 listArguments = rawFilePath$listArguments 109 listArguments = rawFilePath$listArguments
108 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) 110 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
109 md5sumList=list("origin"=getMd5sum(directory)) 111 md5sumList=list("origin"=getMd5sum(directory))