Mercurial > repos > eschen42 > w4mcorcov

comparison w4mcorcov_wrapper.R @ 1:0c2ad44b6c9c draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
author eschen42
date Sun, 22 Oct 2017 18:47:57 -0400
parents 23f9fad4edfc
children e03582f26617
comparison
equal deleted inserted replaced
0:23f9fad4edfc 1:0c2ad44b6c9c
70 my_env$tesC <- as.character(argVc["tesC"]) 70 my_env$tesC <- as.character(argVc["tesC"])
71 my_env$facC <- as.character(argVc["facC"]) 71 my_env$facC <- as.character(argVc["facC"])
72 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) 72 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"])
73 my_env$levCSV <- as.character(argVc["levCSV"]) 73 my_env$levCSV <- as.character(argVc["levCSV"])
74 my_env$matchingC <- as.character(argVc["matchingC"]) 74 my_env$matchingC <- as.character(argVc["matchingC"])
75 my_env$labelFeatures <- as.logical(argVc["labelFeatures"]) 75 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
76
77 label_features <- my_env$labelFeatures
78 labelfeatures_check <- TRUE
79 if ( is.na(label_features) ) {
80 labelfeatures_check <- FALSE
81 } else if ( is.null(label_features) ) {
82 labelfeatures_check <- FALSE
83 } else if (label_features != "ALL") {
84 if ( is.na(as.numeric(label_features)) )
85 labelfeatures_check <- FALSE
86 else if ( as.numeric(label_features) < 0 )
87 labelfeatures_check <- FALSE
88 }
89 if ( !labelfeatures_check ) {
90 my_log("invalid argument: labelFeatures")
91 print(label_features)
92 quit(save = "no", status = 10, runLast = TRUE)
93 }
76 94
77 tsv_action_factory <- function(file, colnames, append) { 95 tsv_action_factory <- function(file, colnames, append) {
78 return ( 96 return (
79 function(tsv) { 97 function(tsv) {
80 write.table( 98 write.table(