--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/circleCor_wrapper.R	Fri Oct 25 07:10:59 2019 -0400
@@ -0,0 +1,102 @@
+#!/usr/bin/env Rscript
+
+# Setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+## Get parameters ##
+suppressPackageStartupMessages(require(argparse))
+
+parser <- ArgumentParser(description='Run the circleCor function')
+
+parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
+parser$add_argument('--blocks_vec', dest='blocks_vec', required=TRUE, help="Blocks vector")
+parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables")
+parser$add_argument('--x_min', dest='x_min', type='double', required=TRUE, help="X min")
+parser$add_argument('--x_max', dest='x_max', type='double', required=TRUE, help="X max")
+parser$add_argument('--y_min', dest='y_min', type='double', required=TRUE, help="Y min")
+parser$add_argument('--y_max', dest='y_max', type='double', required=TRUE, help="Y max")
+parser$add_argument('--output_var', dest='output_var', required=TRUE, help="Output variables file")
+parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
+
+args <- parser$parse_args()
+
+## Print parameters
+print("Input RData:")
+print(args$input_rdata)
+print("Blocks vector:")
+print(args$blocks_vec)
+print("Response variables:")
+print(args$responses_var)
+print("X min:")
+print(args$x_min)
+print("X max:")
+print(args$x_max)
+print("Y min:")
+print(args$y_min)
+print("Y max:")
+print(args$y_max)
+print("Output variables file:")
+print(args$output_var)
+print("Output PDF file:")
+print(args$output_pdf)
+
+## Loading libraries
+suppressPackageStartupMessages(require(ellipse))
+suppressPackageStartupMessages(require(grDevices))
+suppressPackageStartupMessages(require(RColorBrewer))
+# suppressPackageStartupMessages(require(mixOmics))
+
+
+# R script call
+source_local <- function(fname)
+{
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+## Loading local functions
+source_local("Integration_block_splsda_fonc.R")
+
+load(args$input_rdata)
+
+blocks_vector = strsplit(args$blocks_vec, ",")[[1]]
+response_variables = strsplit(args$responses_var, ",")[[1]]
+
+
+print("liste_vec_indice_blockSelect:")
+print(liste_vec_indice_blockSelect)
+print("liste_vec_blocks:")
+print(liste_vec_blocks)
+print("Mat cor comp1:")
+print(mat_cor_comp1)
+print("blocks_vector:")
+print(blocks_vector)
+
+
+
+pdf(args$output_pdf, width=12, height=9)
+
+varSelect = circleCor(liste_dataframe_cor_comp_var_global = liste_dataframe_cor_comp_var_global,
+                      liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
+                      mat_cor_comp1 = mat_cor_comp1,
+                      mat_cor_comp2 = mat_cor_comp2,
+                      vec_blocks = blocks_vector,
+                      nomsVarReponses = response_variables,
+                      min.X = args$x_min,
+                      max.X = args$x_max,
+                      min.Y = args$y_min,
+                      max.Y = args$y_max,
+                      cutoff = 0.85,
+                      rad.in = 0.5,
+                      cex = 0.7,
+                      cex_legend = 0.8,
+                      pos = c(1.2, 0),
+                      pch = 20,
+                      inset = c(-0.25, 0))
+
+dev.off()
+
+write(varSelect, file=args$output_var, ncolumns=1)
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