Mercurial > repos > eschen42 > w4mclassfilter

comparison w4mclassfilter_wrapper.R @ 0:bab3a658f74e draft

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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
author eschen42
date Tue, 09 May 2017 18:34:35 -0400
parents
children 23c6d271def9
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-1:000000000000 0:bab3a658f74e
1 #!/usr/bin/env Rscript
2
3 library(batch) ## parseCommandArgs
4
5 ########
6 # MAIN #
7 ########
8
9 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
10
11 ##------------------------------
12 ## Initializing
13 ##------------------------------
14
15 ## options
16 ##--------
17
18 strAsFacL <- options()$stringsAsFactors
19 options(stringsAsFactors = FALSE)
20
21 ## libraries
22 ##----------
23
24 suppressMessages(library(w4mclassfilter))
25
26 if(packageVersion("w4mclassfilter") < "0.98.0")
27 stop("Please use 'w4mclassfilter' versions of 0.98.0 and above")
28
29 ## constants
30 ##----------
31
32 modNamC <- "w4mclassfilter" ## module name
33
34 topEnvC <- environment()
35 flgC <- "\n"
36
37 ## functions
38 ##----------
39
40 flgF <- function(tesC,
41 envC = topEnvC,
42 txtC = NA) { ## management of warning and error messages
43
44 tesL <- eval(parse(text = tesC), envir = envC)
45
46 if(!tesL) {
47
48 #sink(NULL)
49 stpTxtC <- ifelse(is.na(txtC),
50 paste0(tesC, " is FALSE"),
51 txtC)
52
53 stop(stpTxtC,
54 call. = FALSE)
55
56 }
57
58 } ## flgF
59
60
61 ## log file
62 ##---------
63
64 information <- as.character(argVc["information"])
65
66 #sink(information)
67
68 my_print <- function(x, ...) { cat(c(x, ...))}
69
70 my_print("\nStart of the '", modNamC, "' Galaxy module call: ",
71 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
72
73 ## arguments
74 ##----------
75
76 # files
77
78 dataMatrix_in <- as.character(argVc["dataMatrix_in"])
79 dataMatrix_out <- as.character(argVc["dataMatrix_out"])
80
81 sampleMetadata_in <- as.character(argVc["sampleMetadata_in"])
82 sampleMetadata_out <- as.character(argVc["sampleMetadata_out"])
83
84 variableMetadata_in <- as.character(argVc["variableMetadata_in"])
85 variableMetadata_out <- as.character(argVc["variableMetadata_out"])
86
87 # other parameters
88
89 sampleclassNames <- as.character(argVc["sampleclassNames"])
90 # if (sampleclassNames == "NONE_SPECIFIED") {
91 # sampleclassNames <- as.character(c())
92 #
93 # } else {
94 # sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
95 # }
96 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
97 inclusive <- as.logical(argVc["inclusive"])
98 # print(sprintf("inclusive = '%s'", as.character(inclusive)))
99 classnameColumn <- as.character(argVc["classnameColumn"])
100 samplenameColumn <- as.character(argVc["samplenameColumn"])
101
102 ##------------------------------
103 ## Computation
104 ##------------------------------
105
106 result <- w4m_filter_by_sample_class(
107 dataMatrix_in = dataMatrix_in
108 , sampleMetadata_in = sampleMetadata_in
109 , variableMetadata_in = variableMetadata_in
110 , dataMatrix_out = dataMatrix_out
111 , sampleMetadata_out = sampleMetadata_out
112 , variableMetadata_out = variableMetadata_out
113 , classes = sampleclassNames
114 , include = inclusive
115 , class_column = classnameColumn
116 , samplename_column = samplenameColumn
117 , failure_action = my_print
118 )
119
120 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",
121 as.character(result), "\n", sep = "")
122
123 ##--------
124 ## Closing
125 ##--------
126
127 my_print("\nEnd of '", modNamC, "' Galaxy module call: ",
128 as.character(Sys.time()), "\n", sep = "")
129
130 #sink()
131
132 if (!file.exists(dataMatrix_out)) {
133 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out))
134 }# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) }
135
136 if (!file.exists(variableMetadata_out)) {
137 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out))
138 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) }
139
140 if (!file.exists(sampleMetadata_out)) {
141 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out))
142 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) }
143
144 if( !result ) {
145 stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
146 }
147
148 rm(list = ls())