while(defined ($file = readdir(DIR))) {
    next if $file =~ /^\.\.?$/; 
    if ($file =~ /_s_/) {
      $file = "../human/chr".$c.".fa/$file";
      foreach $tool (@$tools) {
	print $file,"\n";              #  <------ line 1
	 $tool =~ s/<infile>/$file/;   #  <------ line 2
	 print $tool,"\n";             #  <------ line 3
      }
    }
  }