Mercurial > repos > lecorguille > ipo

annotate ipo4retgroup.r @ 1:ae8de756dfcf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
author workflow4metabolomics
date Mon, 16 Dec 2019 05:26:42 -0500
parents ac5f2936575b
children 8e5f667359cb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
1 #!/usr/bin/env Rscript
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
2 #Authors Gildas Le Corguille and Yann Guitton
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
3
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
4
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
5 # ----- PACKAGE -----
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
6 cat("\tSESSION INFO\n")
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
7
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
8 #Import the different functions
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
9 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
10 source_local("lib.r")
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
11
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
12 pkgs <- c("IPO","batch")
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
13 loadAndDisplayPackages(pkgs)
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
14 cat("\n\n");
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
15
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
16
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
17 # ----- ARGUMENTS -----
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
18 cat("\tARGUMENTS INFO\n")
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
19 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
20 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
21
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
22 cat("\n\n");
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
23
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
24
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
25 # ----- PROCESSING INFILE -----
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
26 cat("\tARGUMENTS PROCESSING INFO\n")
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
27
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
28 samplebyclass = 2
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
29 if (!is.null(args$samplebyclass)){
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
30 samplebyclass = args$samplebyclass; args$samplebyclass=NULL
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
31 }
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
32
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
33 cat("\n\n")
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
34
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
35 # ----- INFILE PROCESSING -----
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
36 cat("\tINFILE PROCESSING INFO\n")
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
37 options(bitmapType='cairo')
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
38
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
39 #image is an .RData file necessary to use xset variable given by previous tools
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
40 load(args$image); args$image=NULL
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
41
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
42 # Because so far CAMERA isn't compatible with the new XCMSnExp object
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
43 if (exists("xdata")){
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
44 xset <- getxcmsSetObject(xdata)
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
45 }
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
46
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
47 if (!exists("xset")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata' which is provided by the tool: MSnbase readMSData")
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
48
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
49
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
50 # Handle infiles
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
51 if (!exists("singlefile")) singlefile <- NULL
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
52 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
53 singlefile <- rawFilePath$singlefile
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
54 print(singlefile)
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
55 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL)
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
56
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
57
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
58 cat("\n\n")
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
59
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
60
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
61 # ----- MAIN PROCESSING INFO -----
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
62 cat("\tMAIN PROCESSING INFO\n")
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
63
1
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 0
diff changeset
64 ipo4retgroup(xset, directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
0
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
65
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
66 cat("\n\n")
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
67
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
68
ac5f2936575b planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
lecorguille
parents:
diff changeset
69 cat("\tDONE\n")