Added wrapper script

Author: mcmero

mintie

@@ -0,0 +1,64 @@
+#!/bin/bash
+
+MINTIELOGO=$(cat <<'END'
+  __  __ ___ _   _ _____ ___ _____
+ |  \/  |_ _| \ | |_   _|_ _| ____|
+ | |\/| || ||  \| | | |  | ||  _|
+ | |  | || || |\  | | |  | || |___
+ |_|  |_|___|_| \_| |_| |___|_____|
+
+Method for Inferring Novel Transcripts and Isoforms using Equivalences classes
+END
+)
+
+while [[ $# -gt 0 ]]
+do
+	arg="$1"
+	case $arg in
+        -h)
+        echo "$MINTIELOGO"
+        echo ""
+        echo "MINTIE wrapper script"
+        echo ""
+        echo "Invokes the MINTIE bpipe pileline."
+        echo "See https://github.com/Oshlack/MINTIE/wiki/ for further information on using MINTIE."
+        echo -e "\nusage (info): mintie [-h] "
+        echo -e "\nusage (setup references): mintie -r "
+        echo -e "\nusage (setup test data): mintie -t "
+        echo -e "\nusage (wrapper): mintie -w -p [params.txt] cases/*.fastq.gz controls/*.fastq.gz "
+        echo -e "\nusage (direct):\n export \$MINTIEDIR=$MINTIE_HOME;\n bpipe run -@$MINTIEDIR/params.txt  [ <other bpipe options >] \n\t \$MINTIEDIR/MINTIE.groovy cases/*.fastq.gz controls/*fastq.gz"
+        echo ""
+        exit 0
+        shift
+        ;;
+        -r)
+        echo -e "Generating references...\n"
+        cd $MINTIE_HOME && ./setup_references_hg38.sh ;
+        exit 0
+        shift
+        ;;
+        -t)
+        echo -e "Setting up test data...\n"
+        cp -r $MINTIE_HOME/test/data/c* . ;
+        cp -r $MINTIE_HOME/test/test_params.txt test_params.txt ;
+        exit 0
+        shift
+        ;;
+        -w)
+        ECHO=""
+        shift
+        ;;
+        -p)
+        MINTIEPARAMSFILE=$2
+        shift 
+        shift 
+        ;;
+        *)    # files
+        MINTIEFILES+=("$1") 
+        shift 
+        ;;
+    esac
+done
+
+set -- "${MINTIEFILES[@]}" 
+$ECHO bpipe run @${MINTIEPARAMSFILE} $MINTIE_HOME/MINTIE.groovy "$@"