--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MUMmer/mummer_tool.sh	Tue Mar 31 14:19:49 2015 +0200
@@ -0,0 +1,128 @@
+#!/bin/bash
+## use #!/bin/bash -x for debugging
+
+## Galaxy wrapper for MUMmer (nucmer/promer)
+## Alex Bossers, CVI of Wageningen UR, NL
+## alex_dot_bossers_at_wur_dot_nl
+##
+## Sep 2010
+##
+## Wrapper runs MUMmer nucmer/promer and additional args
+## Calculates the comparison scores (delta and optional coords file)
+## Generates the optional STATIC comparison mummerplot to png (from delta file)
+##
+## finally the script renames (optional) output files to outfiles expected by Galaxy
+##
+##
+## INPUT args:
+## nucmer_tool.sh $input_ref $input_query $out_delta $out_coords $out_png $logfile 
+##                    @0          @1          @2          @3        @4       @5   
+##                $algorithm $keep_delta $make_coords $keep_log $make_image $cmd_extra 
+##                     @6        @7           @8          @9        @10         @11
+##
+
+# Function to send error messages.
+log_err() { echo "$@" 1>&2; }
+# path to where mummer suite is installed
+# adjust this for your machine
+# If mummer is available in system path, leave empty
+# when using different path make sure the trailing slash is added.
+# mum_path = /opt/Mummer23/Mummer/
+mum_path=""
+tmp_path="/tmp/mummertmp/"
+
+if [ $num_path"$(which mummer)" == "" ] && [ "$num_path" == "" ]; then
+	log_err "mummer is not available in system path and not declarated in mum_path. Please install mummer."
+	exit 127 
+fi
+
+# since we have more than 9 arguments we need to shift the sections or use own array
+args=("$@")
+# to keep things readible assign vars
+input_ref="${args[0]}"
+input_query="${args[1]}"
+out_delta="${args[2]}"
+out_coords="${args[3]}"
+out_png="${args[4]}"
+logfile="${args[5]}"
+algorithm="${args[6]}"
+keep_delta="${args[7]}"
+make_coords="${args[8]}"
+keep_log="${args[9]}"
+make_image="${args[10]}"
+cmd_extra="${args[11]}"
+
+[ -d $tmp_path ] || mkdir $tmp_path
+cd $tmp_path
+
+# enable/disable the STDOUT log file
+if [ "$keep_log" == "yes" ]; then
+	logfile_c="2>$logfile"
+	logfile_a="2>>$logfile"
+else
+	#dump to dev/null
+	logfile_c="2>&-"
+	logfile_a="2>&-"
+fi
+
+# extra mummer cmd line options
+
+## generate coords file on the fly?
+if [ "$make_coords" == "yes" ]; then
+	options=" --coords"
+fi
+## extra cmd line args to be concatenated in options? We need to prevent extra spaces!
+if [ "$cmd_extra" != "" ]; then
+	if [ "$options" == "" ]; then
+		options=" $cmd_extra"
+	else
+		options="$options $cmd_extra"
+	fi
+fi
+
+# run nucmer/promer
+# May only run Promer and Nucmer
+echo $algorithm
+if [[ $algorithm =~ ...mer$ ]]; then
+	eval "$mum_path$algorithm$options $input_ref $input_query $logfile_c"
+else 
+	log_err 'ERROR, algorithm does not conform to ...mer'
+	exit 1
+fi
+
+
+## generate large png if option make_image = yes
+## suppress error from mummerplot since some is deprecated but not a real error
+## error can be easily avoided by modifying the source of mummerplot... just in case
+## however we need to check if a valid png was generated. This is not the case is alignment is none
+## 1 is stderr and 2 stdout. redirect to dev/null
+if [ "${make_image}" == "yes" ]; then
+	eval "$mum_path mummerplot --large --png out.delta 1>&- $logfile_a"
+	if [ -f "out.png" ]; then
+		mv out.png $out_png
+		#cleanup temp gnuplot file
+		rm out.gp
+	else
+		log_err "not exist the req png file!"
+		exit 1
+	fi
+	
+	## clean up remaining files
+	rm out.fplot
+	rm out.rplot
+
+fi
+
+# keep/rename or delete delta file
+if [ "$keep_delta" == "yes" ]; then
+	mv out.delta "$out_delta" 
+else
+	rm out.delta
+fi
+
+# keep/rename coords file if it was created
+if [ "$make_coords" == "yes" ]; then
+	mv out.coords "$out_coords"
+fi
+# end script
+exit 0
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