--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abacas.sh	Thu Nov 21 12:53:20 2019 -0500
@@ -0,0 +1,77 @@
+#!/bin/bash
+
+#wrapper for abacas
+##our arguments will come in as an array
+
+args=("$@")
+
+#to keep things readable assign vars
+input_ref="${args[0]}"
+input_query="${args[1]}"
+ordered_contigs="${args[2]}"
+use_bin="${args[3]}"
+non="${args[4]}"
+append_bin="${args[5]}"
+out_bin="${args[6]}"
+out_crunch="${args[7]}"
+out_gaps="${args[8]}"
+out_fasta="${args[9]}"
+out_tab="${args[10]}"
+out_unused="${args[11]}"
+out_multi="${args[12]}"
+out_binmulti="${args[13]}"
+out_nonpseudo="${args[14]}"
+
+##ok lets do up the optional tags.....I have four thus far
+##generate ordered multifasta file
+
+if [ "$ordered_contigs" == "yes" ]; then
+	options="-m"
+fi
+
+if [ "$use_bin" == "yes" ]; then
+        options="$options -b"
+fi
+
+if [ "$non" == "yes" ]; then
+        options="$options -N"
+fi
+
+if [ "$append_bin" == "yes" ]; then
+        options="$options -a"
+fi
+
+options="$options -o ab_out"
+
+script_path="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"
+
+#run abacas
+eval "perl $script_path/abacas.1.1.pl $options -r $input_ref -q $input_query -p nucmer"
+echo "perl $script_path/abacas.1.1.pl $options -r $input_ref -q $input_query -p nucmer"
+#ok now we have to remove the nucmer files to cleanup a bit...
+rm nucmer.delta
+rm nucmer.filtered.delta
+rm nucmer.tiling
+
+#name the datafiles properly
+mv ab_out.bin "$out_bin"
+if [ "$ordered_contigs" == "yes" ]; then
+	mv ab_out.contigs.fas "$out_multi"
+fi
+
+if [ "$use_bin" == "yes" ]; then
+	mv ab_out.contigsInbin.fas "$out_binmulti"
+fi
+
+mv ab_out.crunch "$out_crunch"
+mv ab_out.fasta "$out_fasta"
+mv ab_out.gaps "$out_gaps"
+
+if [ "$non" == "yes" ]; then
+	mv ab_out.NoNs.fasta "$out_nonpseudo"
+fi
+
+mv ab_out.tab "$out_tab"
+mv unused_contigs.out "$out_unused"
+
+#end script for now