comparison w4mcorcov_wrapper.R @ 14:90708fdbc22d draft default tip

"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"

13:2ae2d26e3270

# This script assumes that it is being executed in a current working directory containing the following files:
#   - w4mcorcov_lib.R
#   - w4mcorcov_input.R
#   - w4mcorcov_calc.R

## constants
##----------

modNamC <- "w4mcorcov" ## module name

my_env$facC               <- as.character(argVc["facC"])
my_env$pairSigFeatOnly    <- as.logical(argVc["pairSigFeatOnly"])
my_env$levCSV             <- as.character(argVc["levCSV"])
my_env$matchingC          <- as.character(argVc["matchingC"])
my_env$labelFeatures      <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
my_env$fdr_features       <- as.character(argVc["fdr_features"]) # number of features to consider when adjusting p-value, or 'ALL'
my_env$cplot_o            <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested
my_env$cplot_p            <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested
my_env$cplot_y            <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot

    labelfeatures_check <- FALSE
}
if ( !labelfeatures_check ) {
  my_log("invalid argument: labelFeatures")
  print(label_features)
  quit(save = "no", status = 10, runLast = TRUE)
}

corcov_tsv_colnames <- TRUE
corcov_tsv_append   <- FALSE

14:90708fdbc22d

# This script assumes that it is being executed in a current working directory containing the following files:
#   - w4mcorcov_lib.R
#   - w4mcorcov_input.R
#   - w4mcorcov_calc.R
options(warn=1)
## constants
##----------

modNamC <- "w4mcorcov" ## module name

my_env$facC               <- as.character(argVc["facC"])
my_env$pairSigFeatOnly    <- as.logical(argVc["pairSigFeatOnly"])
my_env$levCSV             <- as.character(argVc["levCSV"])
my_env$matchingC          <- as.character(argVc["matchingC"])
my_env$labelFeatures      <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
my_env$min_crossval_i     <- as.character(argVc["min_crossval_i"]) # Minumum number of samples for OPLS-DA cross-validation
my_env$fdr_features       <- as.character(argVc["fdr_features"]) # number of features to consider when adjusting p-value, or 'ALL'
my_env$cplot_o            <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested
my_env$cplot_p            <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested
my_env$cplot_y            <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot

    labelfeatures_check <- FALSE
}
if ( !labelfeatures_check ) {
  my_log("invalid argument: labelFeatures")
  print(label_features)
  quit(save = "no", status = 10, runLast = TRUE)
}

min_crossval_i <- my_env$min_crossval_i
crossval_check <- TRUE
if ( is.na(min_crossval_i) ) {
  crossval_check <- FALSE
} else if ( is.null(min_crossval_i) ) {
  crossval_check <- FALSE
} else {
  if ( is.na(as.numeric(min_crossval_i)) )
    crossval_check <- FALSE
  else if ( as.numeric(min_crossval_i) < 0 )
    crossval_check <- FALSE
}
if ( !crossval_check ) {
  my_log("invalid argument: min_crossval_i")
  print(min_crossval_i)
  quit(save = "no", status = 10, runLast = TRUE)
}

corcov_tsv_colnames <- TRUE
corcov_tsv_append   <- FALSE