Mercurial > repos > tomnl > assess_purity_msms

annotate frag4feature.R @ 1:c694d8172abf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Tue, 27 Mar 2018 05:41:35 -0400
parents b6b051e7a5ef
children 146699c00d38
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
1 library(optparse)
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
2 library(msPurity)
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
3 library(xcms)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
4
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
5 xset_pa_filename_fix <- function(opt, pa, xset){
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
6
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
7
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
8 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
9 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
10 # needs to be done due to Galaxy moving the files around and screwing up any links to files
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
11
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
12 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
13 filepaths <- filepaths[filepaths != ""]
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
14 new_names <- basename(filepaths)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
15
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
16 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
17 galaxy_names <- galaxy_names[galaxy_names != ""]
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
18
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
19 nsave <- names(pa@fileList)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
20 old_filenames <- basename(pa@fileList)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
21 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
22 names(pa@fileList) <- nsave
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
23
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
24 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
25 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
26 }
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
27
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
28
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
29 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
30 if(!all(names(pa@fileList)==basename(xset@filepaths))){
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
31 print('FILELISTS DO NOT MATCH')
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
32 message('FILELISTS DO NOT MATCH')
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
33 quit(status = 1)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
34 }else{
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
35 xset@filepaths <- unname(pa@fileList)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
36 }
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
37 }
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
38
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
39
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
40 return(list(pa, xset))
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
41 }
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
42
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
43
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
44 option_list <- list(
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
45 make_option(c("-o", "--out_dir"), type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
46 make_option("--pa", type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
47 make_option("--xset", type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
48 make_option("--ppm", default=10),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
49 make_option("--plim", default=0.0),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
50 make_option("--convert2RawRT", action="store_true"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
51 make_option("--mostIntense", action="store_true"),
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
52 make_option("--createDB", action="store_true"),
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
53 make_option("--cores", default=4),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
54 make_option("--mzML_files", type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
55 make_option("--galaxy_names", type="character"),
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
56 make_option("--grp_peaklist", type="character")
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
57 )
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
58
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
59 # store options
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
60 opt<- parse_args(OptionParser(option_list=option_list))
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
61
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
62 loadRData <- function(rdata_path, name){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
63 #loads an RData file, and returns the named xset object if it is there
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
64 load(rdata_path)
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
65 return(get(ls()[ls() == name]))
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
66 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
67
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
68 # Requires
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
69 pa <- loadRData(opt$pa, 'pa')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
70 xset <- loadRData(opt$xset, 'xset')
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
71
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
72 pa@cores <- opt$cores
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
73
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
74 print(pa@fileList)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
75 print(xset@filepaths)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
76
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
77 if(is.null(opt$mostIntense)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
78 mostIntense = FALSE
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
79 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
80 mostIntense = TRUE
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
81 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
82
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
83 if(is.null(opt$convert2RawRT)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
84 convert2RawRT = FALSE
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
85 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
86 convert2RawRT= TRUE
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
87 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
88
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
89 if(is.null(opt$createDB)){
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
90 createDB = FALSE
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
91 }else{
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
92 createDB = TRUE
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
93 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
94
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
95
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
96 fix <- xset_pa_filename_fix(opt, pa, xset)
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
97 pa <- fix[[1]]
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
98 xset <- fix[[2]]
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
99
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
100 if(is.null(opt$grp_peaklist)){
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
101 grp_peaklist = NA
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
102
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
103
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
104 }else{
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
105 grp_peaklist = opt$grp_peaklist
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
106 }
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
107
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
108 print('heck')
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
109 print(pa@fileList)
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
110 print(names(pa@fileList))
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
111 print(xset@filepaths)
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
112 saveRDS(pa, 'test_pa.rds')
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
113
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
114 pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$ppm, plim=opt$plim,
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
115 intense=opt$mostIntense, convert2RawRT=convert2RawRT,
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
116 db_name='alldata.sqlite', out_dir=opt$out_dir, grp_peaklist=grp_peaklist,
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
117 create_db=createDB)
0
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
118
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
119 save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
120
b6b051e7a5ef planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
121 print(head(pa@grped_df))
1
c694d8172abf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
122 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature.tsv'), row.names=FALSE, sep='\t')