Mercurial > repos > lecorguille > xcms_retcor
annotate lib.r @ 8:4bfef820569b draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author | lecorguille |
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date | Fri, 07 Apr 2017 07:36:24 -0400 |
parents | bb602a5b8819 |
children | 8828cba9aedd |
rev | line source |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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1 #Authors ABiMS TEAM |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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2 #Lib.r for Galaxy Workflow4Metabolomics xcms tools |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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3 # |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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4 #version 2.4: lecorguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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5 # add getPeaklistW4M |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
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6 #version 2.3: yguitton |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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7 # correction for empty PDF when only 1 class |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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8 #version 2.2 |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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9 # correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
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10 # Note if scanrange is used a warning is prompted in R console but do not stop PDF generation |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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11 #version 2.1: yguitton |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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12 # Modifications made by Guitton Yann |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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13 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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14 |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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15 #@author G. Le Corguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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16 #This function convert if it is required the Retention Time in minutes |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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17 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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18 if (convertRTMinute){ |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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19 #converting the retention times (seconds) into minutes |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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20 print("converting the retention times into minutes in the variableMetadata") |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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21 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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22 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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23 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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24 } |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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25 return (variableMetadata) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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26 } |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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27 |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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28 #@author G. Le Corguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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29 #This function format ions identifiers |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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7
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30 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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31 splitDeco = strsplit(as.character(variableMetadata$name),"_") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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32 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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33 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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34 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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35 return(variableMetadata) |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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36 } |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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37 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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38 #@author G. Le Corguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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39 # value: intensity values to be used into, maxo or intb |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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40 getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) { |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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41 variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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42 variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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43 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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44 dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))] |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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45 |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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46 variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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47 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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48 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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49 |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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50 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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51 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) |
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bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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52 } |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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53 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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54 #@author Y. Guitton |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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55 getBPC <- function(file,rtcor=NULL, ...) { |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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56 object <- xcmsRaw(file) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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57 sel <- profRange(object, ...) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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58 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE])) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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59 #plotChrom(xcmsRaw(file), base=T) |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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60 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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61 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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62 #@author Y. Guitton |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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63 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) { |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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64 cat("Creating BIC pdf...\n") |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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65 |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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66 if (is.null(xcmsSet)) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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67 cat("Enter an xcmsSet \n") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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68 stop() |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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69 } else { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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70 files <- filepaths(xcmsSet) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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71 } |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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72 |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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73 phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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74 |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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75 classnames<-vector("list",length(phenoDataClass)) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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76 for (i in 1:length(phenoDataClass)){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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77 classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i]) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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78 } |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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79 |
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4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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80 N <- dim(phenoData(xcmsSet))[1] |
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81 |
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82 TIC <- vector("list",N) |
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83 |
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84 |
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85 for (j in 1:N) { |
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86 |
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87 TIC[[j]] <- getBPC(files[j]) |
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88 #good for raw |
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89 # seems strange for corrected |
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90 #errors if scanrange used in xcmsSetgeneration |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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91 if (!is.null(xcmsSet) && rt == "corrected") |
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92 rtcor <- xcmsSet@rt$corrected[[j]] |
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93 else |
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94 rtcor <- NULL |
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95 |
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96 TIC[[j]] <- getBPC(files[j],rtcor=rtcor) |
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97 # TIC[[j]][,1]<-rtcor |
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98 } |
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99 |
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100 |
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101 |
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102 pdf(pdfname,w=16,h=10) |
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103 cols <- rainbow(N) |
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104 lty = 1:N |
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105 pch = 1:N |
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106 #search for max x and max y in BPCs |
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107 xlim = range(sapply(TIC, function(x) range(x[,1]))) |
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108 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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109 ylim = c(-ylim[2], ylim[2]) |
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110 |
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111 |
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112 ##plot start |
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113 |
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114 if (length(phenoDataClass)>2){ |
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115 for (k in 1:(length(phenoDataClass)-1)){ |
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116 for (l in (k+1):length(phenoDataClass)){ |
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117 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" ")) |
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118 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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119 colvect<-NULL |
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120 for (j in 1:length(classnames[[k]])) { |
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121 tic <- TIC[[classnames[[k]][j]]] |
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122 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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123 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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124 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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125 } |
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126 for (j in 1:length(classnames[[l]])) { |
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127 # i=class2names[j] |
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128 tic <- TIC[[classnames[[l]][j]]] |
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129 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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130 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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131 } |
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132 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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133 } |
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134 } |
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135 }#end if length >2 |
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136 |
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137 if (length(phenoDataClass)==2){ |
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138 k=1 |
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139 l=2 |
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140 colvect<-NULL |
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141 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC") |
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142 |
2
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143 for (j in 1:length(classnames[[k]])) { |
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144 |
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145 tic <- TIC[[classnames[[k]][j]]] |
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146 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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147 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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148 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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149 } |
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150 for (j in 1:length(classnames[[l]])) { |
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151 # i=class2names[j] |
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152 tic <- TIC[[classnames[[l]][j]]] |
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153 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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154 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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155 } |
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156 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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157 |
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158 }#end length ==2 |
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159 |
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160 #case where only one class |
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161 if (length(phenoDataClass)==1){ |
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162 k=1 |
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163 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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164 colvect<-NULL |
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165 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC") |
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166 |
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167 for (j in 1:length(classnames[[k]])) { |
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168 tic <- TIC[[classnames[[k]][j]]] |
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169 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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170 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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171 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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172 } |
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173 |
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174 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) |
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175 |
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176 }#end length ==1 |
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177 |
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178 dev.off() #pdf(pdfname,w=16,h=10) |
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179 |
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180 invisible(TIC) |
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181 } |
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182 |
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183 |
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184 |
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185 #@author Y. Guitton |
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186 getTIC <- function(file,rtcor=NULL) { |
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187 object <- xcmsRaw(file) |
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188 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity) |
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189 } |
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190 |
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191 ## |
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192 ## overlay TIC from all files in current folder or from xcmsSet, create pdf |
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193 ## |
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194 #@author Y. Guitton |
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195 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) { |
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196 cat("Creating TIC pdf...\n") |
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197 |
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198 if (is.null(xcmsSet)) { |
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199 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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200 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|") |
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201 if (is.null(files)) |
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202 files <- getwd() |
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203 info <- file.info(files) |
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204 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE) |
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205 files <- c(files[!info$isdir], listed) |
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206 } else { |
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207 files <- filepaths(xcmsSet) |
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208 } |
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209 |
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210 phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class |
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211 classnames<-vector("list",length(phenoDataClass)) |
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212 for (i in 1:length(phenoDataClass)){ |
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213 classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i]) |
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214 } |
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215 |
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216 N <- length(files) |
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217 TIC <- vector("list",N) |
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218 |
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219 for (i in 1:N) { |
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220 if (!is.null(xcmsSet) && rt == "corrected") |
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221 rtcor <- xcmsSet@rt$corrected[[i]] else |
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222 rtcor <- NULL |
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223 TIC[[i]] <- getTIC(files[i],rtcor=rtcor) |
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224 } |
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225 |
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226 pdf(pdfname,w=16,h=10) |
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227 cols <- rainbow(N) |
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228 lty = 1:N |
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229 pch = 1:N |
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230 #search for max x and max y in TICs |
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231 xlim = range(sapply(TIC, function(x) range(x[,1]))) |
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232 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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233 ylim = c(-ylim[2], ylim[2]) |
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234 |
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235 |
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236 ##plot start |
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237 if (length(phenoDataClass)>2){ |
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238 for (k in 1:(length(phenoDataClass)-1)){ |
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239 for (l in (k+1):length(phenoDataClass)){ |
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240 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" ")) |
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241 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC") |
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242 colvect<-NULL |
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243 for (j in 1:length(classnames[[k]])) { |
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244 tic <- TIC[[classnames[[k]][j]]] |
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245 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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246 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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247 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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248 } |
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249 for (j in 1:length(classnames[[l]])) { |
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250 # i=class2names[j] |
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251 tic <- TIC[[classnames[[l]][j]]] |
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252 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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253 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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254 } |
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255 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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256 } |
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257 } |
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258 }#end if length >2 |
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259 if (length(phenoDataClass)==2){ |
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260 k=1 |
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261 l=2 |
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262 |
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263 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC") |
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264 colvect<-NULL |
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265 for (j in 1:length(classnames[[k]])) { |
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266 tic <- TIC[[classnames[[k]][j]]] |
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267 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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268 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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269 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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270 } |
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271 for (j in 1:length(classnames[[l]])) { |
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272 # i=class2names[j] |
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273 tic <- TIC[[classnames[[l]][j]]] |
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274 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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275 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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276 } |
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277 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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278 |
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279 }#end length ==2 |
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280 |
8
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281 #case where only one class |
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282 if (length(phenoDataClass)==1){ |
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283 k=1 |
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284 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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285 |
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286 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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287 colvect<-NULL |
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288 for (j in 1:length(classnames[[k]])) { |
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289 tic <- TIC[[classnames[[k]][j]]] |
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290 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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291 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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292 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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293 } |
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294 |
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295 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) |
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296 |
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297 }#end length ==1 |
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298 |
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299 dev.off() #pdf(pdfname,w=16,h=10) |
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300 |
8
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301 invisible(TIC) |
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302 } |
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303 |
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304 |
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305 |
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306 ## |
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307 ## Get the polarities from all the samples of a condition |
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308 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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309 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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310 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
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311 cat("Creating the sampleMetadata file...\n") |
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312 |
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313 #Create the sampleMetada dataframe |
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314 sampleMetadata=xset@phenoData |
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315 sampleNamesOrigin=rownames(sampleMetadata) |
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316 sampleNamesMakeNames=make.names(sampleNamesOrigin) |
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317 |
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318 if (any(duplicated(sampleNamesMakeNames))) { |
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319 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr()) |
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320 for (sampleName in sampleNamesOrigin) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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321 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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322 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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323 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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324 } |
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325 |
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326 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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327 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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328 for (sampleName in sampleNamesOrigin) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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329 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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330 } |
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331 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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332 |
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333 sampleMetadata$sampleMetadata=sampleNamesMakeNames |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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334 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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335 rownames(sampleMetadata)=NULL |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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336 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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337 #Create a list of files name in the current directory |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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338 list_files=xset@filepaths |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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339 #For each sample file, the following actions are done |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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340 for (file in list_files){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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341 #Check if the file is in the CDF format |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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342 if (!mzR:::netCDFIsFile(file)){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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343 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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344 # If the column isn't exist, with add one filled with NA |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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345 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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346 |
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347 #Create a simple xcmsRaw object for each sample |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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348 xcmsRaw=xcmsRaw(file) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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349 #Extract the polarity (a list of polarities) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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350 polarity=xcmsRaw@polarity |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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351 #Verify if all the scans have the same polarity |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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352 uniq_list=unique(polarity) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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353 if (length(uniq_list)>1){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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354 polarity="mixed" |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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355 } else { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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356 polarity=as.character(uniq_list) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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357 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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358 #Transforms the character to obtain only the sample name |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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359 filename=basename(file) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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360 library(tools) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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361 samplename=file_path_sans_ext(filename) |
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362 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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363 #Set the polarity attribute |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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364 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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365 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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366 #Delete xcmsRaw object because it creates a bug for the fillpeaks step |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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367 rm(xcmsRaw) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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368 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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369 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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370 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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371 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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372 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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373 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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374 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames)) |
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375 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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376 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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377 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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378 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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379 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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380 ## This function check if xcms will found all the files |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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381 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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382 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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383 checkFilesCompatibilityWithXcms <- function(directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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384 cat("Checking files filenames compatibilities with xmcs...\n") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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385 # WHAT XCMS WILL FIND |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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386 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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387 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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388 info <- file.info(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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389 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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390 files <- c(directory[!info$isdir], listed) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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391 files_abs <- file.path(getwd(), files) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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392 exists <- file.exists(files_abs) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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393 files[exists] <- files_abs[exists] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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394 files[exists] <- sub("//","/",files[exists]) |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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395 |
8
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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396 # WHAT IS ON THE FILESYSTEM |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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397 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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398 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
399 |
8
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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400 # COMPARISON |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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401 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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402 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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403 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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diff
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404 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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405 } |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff
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|
406 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff
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|
407 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff
changeset
|
408 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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409 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
410 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
411 ## This function check if XML contains special caracters. It also checks integrity and completness. |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
412 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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changeset
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413 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
|
414 checkXmlStructure <- function (directory) { |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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415 cat("Checking XML structure...\n") |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
416 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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417 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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418 capture=system(cmd,intern=TRUE) |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
|
419 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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parents:
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diff
changeset
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420 if (length(capture)>0){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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421 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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422 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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423 write(capture, stderr()) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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changeset
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424 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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425 } |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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426 |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff
changeset
|
427 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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428 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
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429 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
430 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
431 ## This function check if XML contain special characters |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
432 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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433 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
|
434 deleteXmlBadCharacters<- function (directory) { |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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changeset
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435 cat("Checking Non ASCII characters in the XML...\n") |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
|
436 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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437 processed=F |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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438 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff
changeset
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439 for (i in l){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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440 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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441 capture=suppressWarnings(system(cmd,intern=TRUE)) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
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442 if (length(capture)>0){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
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443 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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444 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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445 c=system(cmd,intern=TRUE) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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446 capture="" |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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447 processed=T |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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changeset
|
448 } |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
449 } |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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parents:
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changeset
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450 if (processed) cat("\n\n") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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451 return(processed) |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
452 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
453 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff
changeset
|
454 |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
changeset
|
455 ## |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
456 ## This function will compute MD5 checksum to check the data integrity |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
457 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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458 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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459 getMd5sum <- function (directory) { |
8
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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changeset
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460 cat("Compute md5 checksum...\n") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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461 # WHAT XCMS WILL FIND |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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462 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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463 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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464 info <- file.info(directory) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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465 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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466 files <- c(directory[!info$isdir], listed) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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467 exists <- file.exists(files) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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468 files <- files[exists] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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|
469 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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|
470 library(tools) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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|
471 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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472 #cat("\n\n") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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|
473 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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474 return(as.matrix(md5sum(files))) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
475 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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changeset
|
476 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
477 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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changeset
|
478 # This function get the raw file path from the arguments |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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changeset
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479 getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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480 if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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481 if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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482 if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
483 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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|
484 if (!is.null(listArguments[["singlefile_galaxyPath"]])) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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485 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]]; |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
486 singlefile_sampleNames = listArguments[["singlefile_sampleName"]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
487 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
488 if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
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489 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]]; |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
490 singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
491 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
492 if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
493 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]]; |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
494 singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
495 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
496 if (exists("singlefile_galaxyPaths")){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
497 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,",")) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
498 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,",")) |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
499 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
500 singlefile=NULL |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
501 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
502 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
503 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
504 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
505 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
506 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
507 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
508 listArguments[[argument]]=NULL |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
509 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
510 return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments)) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
511 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
512 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
513 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
514 # This function retrieve the raw file in the working directory |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
515 # - if zipfile: unzip the file with its directory tree |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
516 # - if singlefiles: set symlink with the good filename |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
517 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
518 if(!is.null(singlefile) && (length("singlefile")>0)) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
519 for (singlefile_sampleName in names(singlefile)) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
520 singlefile_galaxyPath = singlefile[[singlefile_sampleName]] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
521 if(!file.exists(singlefile_galaxyPath)){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
522 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
523 print(error_message); stop(error_message) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
524 } |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
525 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
526 file.symlink(singlefile_galaxyPath,singlefile_sampleName) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
527 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
528 directory = "." |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
529 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
530 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
531 if(!is.null(zipfile) && (zipfile!="")) { |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
532 if(!file.exists(zipfile)){ |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
533 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
534 print(error_message) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
535 stop(error_message) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
536 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
537 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
538 #list all file in the zip file |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
539 #zip_files=unzip(zipfile,list=T)[,"Name"] |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
540 |
8
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
541 #unzip |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
542 suppressWarnings(unzip(zipfile, unzip="unzip")) |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
543 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
544 #get the directory name |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
545 filesInZip=unzip(zipfile, list=T); |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
546 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
547 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
548 directory = "." |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
549 if (length(directories) == 1) directory = directories |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
550 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
551 cat("files_root_directory\t",directory,"\n") |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
552 |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
553 } |
4bfef820569b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
7
diff
changeset
|
554 return (directory) |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
555 } |