#!/usr/bin/perl

# Wrapper script written by: Roger Ngo, Sam Min and Todd H. Oakley, UCSB

use warnings;
use strict;
use Cwd;

my $dir = getcwd();

my $iAssemblerBinPath = '/labdata/nfs/galaxy/pkgs/iAssembler';
my $iAssemblerToolPath = '/labdata/nfs/galaxy/galaxy-dist/tools/iAssembler';

#iAssembler_wrapper.pl -i $input -e $maxlength -h $minoverlap -p $minpercent  ...example

my $input=$ARGV[1];
my $maxlength=$ARGV[3];
my $minoverlap=$ARGV[5];
my $minpercent=$ARGV[7];

open my $file, '<', $iAssemblerToolPath."\/increment.txt";
	my $increment = <$file>;
	$increment = int($increment);
close $file;

my $temp = $increment;

open(UPDATE, '>'.$iAssemblerToolPath."\/increment.txt");
	$increment = $increment + 1;
	print UPDATE $increment;
close(UPDATE);

qx/cp $input $iAssemblerBinPath\/input.$temp.fasta/;

chdir($iAssemblerBinPath);

qx/$iAssemblerBinPath\/iAssembler.pl -i input.$temp.fasta -e $maxlength -h $minoverlap -p $minpercent/;

chdir("$dir");

qx/cp $iAssemblerBinPath\/input.$temp.fasta_output\/unigene_seq.fasta unigene_seq.fasta/;

qx/rm -rf $iAssemblerBinPath\/input.$temp.*/;