Mercurial > repos > eschen42 > w4mcorcov

comparison w4mcorcov_wrapper.R @ 2:a06344808ffc draft

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 ce5178ce51b80f242d24db555044e6afc530ac99
author eschen42
date Sat, 11 Nov 2017 00:08:20 -0500
parents e25fd8a13665
children 0b49916c5c52
comparison
equal deleted inserted replaced
1:e25fd8a13665 2:a06344808ffc
65 my_env$contrast_salience <- as.character(argVc["contrast_salience"]) 65 my_env$contrast_salience <- as.character(argVc["contrast_salience"])
66 # print(sprintf("contrast_salience: %s", my_env$contrast_salience)) 66 # print(sprintf("contrast_salience: %s", my_env$contrast_salience))
67 67
68 # other parameters 68 # other parameters
69 69
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 my_env$labelOrthoFeatures <- as.logical(argVc["labelOrthoFeatures"])
77
78 label_features <- my_env$labelFeatures
79 labelfeatures_check <- TRUE
80 if ( is.na(label_features) ) {
81 labelfeatures_check <- FALSE
82 } else if ( is.null(label_features) ) {
83 labelfeatures_check <- FALSE
84 } else if (label_features != "ALL") {
85 if ( is.na(as.numeric(label_features)) )
86 labelfeatures_check <- FALSE
87 else if ( as.numeric(label_features) < 0 )
88 labelfeatures_check <- FALSE
89 }
90 if ( !labelfeatures_check ) {
91 my_log("invalid argument: labelFeatures")
92 print(label_features)
93 quit(save = "no", status = 10, runLast = TRUE)
94 }
76 95
77 tsv_action_factory <- function(file, colnames, append) { 96 tsv_action_factory <- function(file, colnames, append) {
78 return ( 97 return (
79 function(tsv) { 98 function(tsv) {
80 write.table( 99 write.table(