Mercurial > repos > eschen42 > w4mcorcov

comparison w4mcorcov_wrapper.R @ 7:ca9938f2eb6a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
author eschen42
date Tue, 17 Nov 2020 23:29:59 +0000
parents 0b49916c5c52
children
comparison
equal deleted inserted replaced
6:0b49916c5c52 7:ca9938f2eb6a
2 2
3 # This script assumes that it is being executed in a current working directory containing the following files: 3 # This script assumes that it is being executed in a current working directory containing the following files:
4 # - w4mcorcov_lib.R 4 # - w4mcorcov_lib.R
5 # - w4mcorcov_input.R 5 # - w4mcorcov_input.R
6 # - w4mcorcov_calc.R 6 # - w4mcorcov_calc.R
7 7 options(warn=1)
8 ## constants 8 ## constants
9 ##---------- 9 ##----------
10 10
11 modNamC <- "w4mcorcov" ## module name 11 modNamC <- "w4mcorcov" ## module name
12 12
71 ######## 71 ########
72 # MAIN # 72 # MAIN #
73 ######## 73 ########
74 74
75 errorPrint(sessionInfo()) 75 errorPrint(sessionInfo())
76 errorCat("\nsearch path:")
77 errorPrint(search())
78 # errorCat("\nCurrently loaded namespaces:\n")
79 # errorPrint(loadedNamespaces())
76 80
77 argVc <- unlist(parseCommandArgs(evaluate=FALSE)) 81 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
78 errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n") 82 errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n")
79 errorPrint(argVc) 83 errorPrint(argVc)
80 84
102 my_env$facC <- as.character(argVc["facC"]) 106 my_env$facC <- as.character(argVc["facC"])
103 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) 107 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"])
104 my_env$levCSV <- as.character(argVc["levCSV"]) 108 my_env$levCSV <- as.character(argVc["levCSV"])
105 my_env$matchingC <- as.character(argVc["matchingC"]) 109 my_env$matchingC <- as.character(argVc["matchingC"])
106 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' 110 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
111 my_env$min_crossval_i <- as.character(argVc["min_crossval_i"]) # Minumum number of samples for OPLS-DA cross-validation
112 my_env$fdr_features <- as.character(argVc["fdr_features"]) # number of features to consider when adjusting p-value, or 'ALL'
107 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested 113 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested
108 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested 114 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested
109 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot 115 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot
110 116
111 label_features <- my_env$labelFeatures 117 label_features <- my_env$labelFeatures
121 labelfeatures_check <- FALSE 127 labelfeatures_check <- FALSE
122 } 128 }
123 if ( !labelfeatures_check ) { 129 if ( !labelfeatures_check ) {
124 my_log("invalid argument: labelFeatures") 130 my_log("invalid argument: labelFeatures")
125 print(label_features) 131 print(label_features)
132 quit(save = "no", status = 10, runLast = TRUE)
133 }
134
135 min_crossval_i <- my_env$min_crossval_i
136 crossval_check <- TRUE
137 if ( is.na(min_crossval_i) ) {
138 crossval_check <- FALSE
139 } else if ( is.null(min_crossval_i) ) {
140 crossval_check <- FALSE
141 } else {
142 if ( is.na(as.numeric(min_crossval_i)) )
143 crossval_check <- FALSE
144 else if ( as.numeric(min_crossval_i) < 0 )
145 crossval_check <- FALSE
146 }
147 if ( !crossval_check ) {
148 my_log("invalid argument: min_crossval_i")
149 print(min_crossval_i)
126 quit(save = "no", status = 10, runLast = TRUE) 150 quit(save = "no", status = 10, runLast = TRUE)
127 } 151 }
128 152
129 corcov_tsv_colnames <- TRUE 153 corcov_tsv_colnames <- TRUE
130 corcov_tsv_append <- FALSE 154 corcov_tsv_append <- FALSE