--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MUMmer/mummerplot_tool.sh	Tue Mar 31 14:19:49 2015 +0200
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+## simple bash to generate mummerplot of MATCH file
+##
+## Galaxy wrapper by Alex Bossers, CVI of Wageningen UR, Lelystad, NL
+## alex_dot_bossers_at_wur_dot_nl
+##
+##
+## needs a rename of the fixed name to something recognised by galaxy
+## needs cleanout of temp files
+##
+## call is mummerplot $format  $in_match $out_file $cmd_extra
+##             $0        $1         $2       $3       $4
+##
+## since mummerplot uses some deprecated syntax which can be fixed in the source
+## we redirect STDERR to dev/null to circumvent errorstatus in galaxy
+## io redirects 0=stdin 1=stdout 2=stderr to dev/null (or &-)
+
+# Function to send error messages.
+log_err() { echo "$@" 1>&2; }
+
+# path to where mummer suite is installed
+# adjust this for your machine
+# this is the only hard coded path in the scripts
+mum_path=""
+
+if [ $num_path"$(which mummer)" == "" ] && [ "$num_path" == "" ]; then
+	log_err "mummer is not available in system path and not declarated in mum_path. Please install mummer."
+	exit 127 
+fi
+
+# some default options to generate a LARGE fixed PNG/POSTSCRIPT image and not an interactive one.
+
+if [ "$1" = "png" ]; then
+	extension="png"
+else
+	extension="ps"
+fi
+
+eval "$mum_path mummerplot --large --$1 $2 1>&- 2>&-"
+if [ -f "out.$extension" ]; then
+	#conditional move to something known by galaxy
+	mv out.$extension $3
+	#remove gnuplot file
+	rm out.gp
+fi
+
+## clean up
+rm out.fplot
+rm out.rplot
+
+#end script