diff w4mcorcov_wrapper.R @ 13:2ae2d26e3270 draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4

--- a/w4mcorcov_wrapper.R	Thu Nov 08 23:06:09 2018 -0500
+++ b/w4mcorcov_wrapper.R	Wed Dec 12 09:20:02 2018 -0500
@@ -73,6 +73,10 @@
 ########
 
 errorPrint(sessionInfo())
+errorCat("\nsearch path:")
+errorPrint(search())
+# errorCat("\nCurrently loaded namespaces:\n")
+# errorPrint(loadedNamespaces())
 
 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
 errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n")
@@ -104,6 +108,7 @@
 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