#!/usr/bin/perl -w

# usage : perl sm_matrice_phylofish.pl <11 files>
# 02/08/2013 - Wrapper dans le cadre du projet Phylofish (Contact : Jerome Monfort)

use strict;
use File::Basename;

my $input_countfile1      = $ARGV[0];
my $input_countfile2      = $ARGV[1];
my $input_countfile3      = $ARGV[2];
my $input_countfile4      = $ARGV[3];
my $input_countfile5      = $ARGV[4];
my $input_countfile6      = $ARGV[5];
my $input_countfile7      = $ARGV[6];
my $input_countfile8      = $ARGV[7];
my $input_countfile9      = $ARGV[8];
my $input_countfile10     = $ARGV[9];
my $input_countfile11     = $ARGV[10];

my $output_matrice        = $ARGV[11];
my $path = dirname($input_countfile1);
my $nb = ($output_matrice=~/galaxy_dataset_(\d+)\.\S+$/);
my $MATRICE = '/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_phylofish/extractCol.pl';
my $cmd = '';
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time); 
my $ALL =  $mday."-".($mon+1)."_".$hour."h".$min."mn".$sec."phylofish".$nb; 

#placer le fichier finalFile.txt dans un repertoire de sortie unique
`cd $path; mkdir PhyloFish_$ALL;`;


#perl extractCol.pl tests/1.txt tests/2.txt tests/3.txt tests/4.txt tests/5.txt tests/6.txt tests/7.txt tests/8.txt tests/9.txt tests/10.txt tests/11.txt
#perl sm_matrice_phylofish.pl tests/1.txt tests/2.txt tests/3.txt tests/4.txt tests/5.txt tests/6.txt tests/7.txt tests/8.txt tests/9.txt tests/10.txt tests/11.txt
$cmd = "cd $path/PhyloFish_$ALL/;(perl $MATRICE $input_countfile1 $input_countfile2 $input_countfile3 $input_countfile4 $input_countfile5 $input_countfile6 $input_countfile7
$input_countfile8 $input_countfile9 $input_countfile10 $input_countfile11) >& ./matrice_phylofish.log 2>&1";
system $cmd;

#Info pour les biologistes
print STDOUT "Voici la commande pour generer la matrice finale de comptage : \n\n $cmd \n\n ";


####################################################################################
#									           #			
#		GALAXY OUTPUT         						   #
#                                                                                  #
####################################################################################
# Recuperation du fichier sortant de statistiques
if (! -e "$path/PhyloFish_$ALL/FinalCount.txt"){print STDERR "Echec lors de la creation de la matrice. \n";}
else {`cp -a "$path/PhyloFish_$ALL/FinalCount.txt" $output_matrice`;}