diff h_clust_galaxy.R @ 0:dc678d2c1976 draft default tip

planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/h_clust_galaxy.R	Thu Jan 18 07:56:33 2018 -0500
@@ -0,0 +1,79 @@
+#!/usr/local/bioinfo/bin/Rscript --vanilla --slave --no-site-file
+
+# R Script producing a hierarchical clustering
+# Input : a file containing a table with numeric values
+#         except for the first column containing sample names
+#         and the first line containing variable names
+#         separator expected is <TAB>
+#
+# Clustering method :
+#         euclidean, correlation, ...
+#
+# Ouptut : a file containing the image of the clustering
+#-----------------------------------------------------------------
+# Authors : sophie.lamarre(at)insa-toulouse.fr
+#           ignacio.gonzalez(at)toulouse.inra.fr
+#           luc.jouneau(at)inra.fr
+#           valentin.marcon(at)inra.fr
+# Version : 0.9
+# Date    : 06/09/2017
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+##------------------------------
+## Libraries laoding
+##------------------------------
+# For parseCommandArgs function
+library(batch) 
+
+# 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="/"))
+}
+
+#Import the different functions used for the hierarchical clustering
+source_local("h_clust.R")
+
+##------------------------------
+## Lecture parametres
+##------------------------------
+argLs <- parseCommandArgs(evaluate=FALSE)
+
+group_member_file=argLs[["group_member_file"]]
+if (group_member_file=="NO"){
+    group_member_file<-NULL
+}
+select=argLs[["select"]]
+if (select=="NULL"){
+    select<-NULL
+}
+column_clustering=argLs[["column_clustering"]]
+if (column_clustering=="TRUE"){
+    column_clustering<-TRUE
+} else {
+    column_clustering<-FALSE
+}
+
+h_clust(input_file=argLs[["input_file"]],
+     group_member_file=group_member_file,
+     output_file=argLs[["output_file"]],
+     log_file=argLs[["log_file"]],
+     format_image_out=argLs[["format_image_out"]],
+     distance_method=argLs[["distance_method"]],
+     agglomeration_method=argLs[["agglomeration_method"]],
+     column_clustering=column_clustering,
+     select=select,
+     plot_title=argLs[["plot_title"]],
+     xlab=argLs[["xlab"]],
+     ylab=argLs[["ylab"]],
+     width=argLs[["width"]],
+     height=argLs[["height"]],
+     ppi=argLs[["ppi"]],
+     na_encoding=argLs[["NA_code"]])