documentation changes

bin/1.2_filter_motifs/compareBed.sh

@@ -125,7 +125,7 @@ then
 	echo "              -max --max          maximum size of footprints; default is 80"
 	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.bed.fasta"
 	echo "              -h --help           shows this help message"
-	echo "              -p --path           the path where the required scripts merge.R and maxScore.R are stored. Default: same path as this scripts path"
+	echo "              -p --path           the path where the required script compareBed_runinfo.R is stored. Default: same path as this scripts path"
 exit 0
 fi
 
@@ -139,7 +139,7 @@ echo fasta: $fasta \(required\)
 echo min: $min
 echo max: $max
 echo output: $output
-echo path of scripts: $path
+echo relative path of subscript: $path
 
 # check required parameters
 if [ -z $data ] || [ -z $motifs ] || [ -z $fasta ]
@@ -190,7 +190,7 @@ done
 if [ $all_empty == true ]
 	then
 		echo ERROR
-		echo All motiffiles were empty!
+		echo All motiffiles have less than 2 lines!
 		echo Fix motiffiles and try again.
 		exit 1
 fi