Mercurial > repos > lecorguille > xcms_export_samplemetadata
annotate xcms_export_samplemetadata.r @ 9:94eb263cfab4 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
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date | Wed, 07 Apr 2021 09:53:54 +0000 |
parents | 8c62030a1136 |
children | cdab04a1d1d7 |
rev | line source |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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1 #!/usr/bin/env Rscript |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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2 |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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3 #Import the different functions |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
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4 source_local <- function(fname) { |
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
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5 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) |
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
changeset
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6 } |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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7 source_local("lib.r") |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
8 |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
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9 pkgs <- c("xcms", "batch") |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
10 loadAndDisplayPackages(pkgs) |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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11 cat("\n\n"); |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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12 |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
changeset
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13 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
14 |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
15 |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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16 sampleMetadata <- NULL |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
changeset
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17 for (image in args$images) { |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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18 load(image) |
2
942ffa3c38b8
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ba2a5c2e962a95155c344dc1864a9c76eb565e9c
lecorguille
parents:
1
diff
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19 if (exists("raw_data")) xdata <- raw_data |
942ffa3c38b8
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ba2a5c2e962a95155c344dc1864a9c76eb565e9c
lecorguille
parents:
1
diff
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20 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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21 if (is.null(sampleMetadata)) |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
22 sampleMetadata <- xdata@phenoData@data |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
23 else |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
changeset
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24 sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data) |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
25 } |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
changeset
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26 colnames(sampleMetadata) <- c("sample_name", "class") |
1
008aceb33627
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86-dirty
lecorguille
parents:
0
diff
changeset
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27 sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name) |
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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28 |
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
29 # Create a sampleMetada file |
9
94eb263cfab4
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
4
diff
changeset
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30 write.table(sampleMetadata, file = "sampleMetadata.tsv", sep = "\t", row.names = FALSE, quote = FALSE) |