// if uploading a tsv indicated by the POST['type']
if ($_POST['type'] == 'tsv' or $_POST['type'] == 'csv' or $_POST['type'] == 'txt') {
// get clustering parameters
$method = $_POST['method'];
$metric = $_POST['metric'];
$output = 'phyloxml';
//create an xml file
$title = $_POST['title'];
$type = $_POST['type'];
$p = $_POST['p'];
# $addLabels = $addLabels;
# $labelFile = $labelFile;
// build the argument string for Rscript
// flags do nothing,
// future: make flags work, right now, R script assumes current order
$rArgs = "-f {$infile} -m {$method} -d {$metric} -o {$output} -t \"{$title}\" \n\t-p {$p} -s {$type} -l {$labelFile}";
// the file name is the expected output of clustr.r
$stdout = callR("clustr.r", "{$rArgs}");
$stdout = explode(",<r>,", $stdout);
$file = $stdout[0];
$rowlabels = $stdout[1];
$out = openfile($file, "b");
//give the file to the user to download
// $name = $_FILES['file']['name'];
$name = $title;
require "download.php";
// download script
downloadFile($file, "{$name}.xml");
// and exit so nothing else is sent back to the browser
exit;
}
$pattern = '/[^a-zA-Z0-9]/';
$dataset = preg_replace($pattern, "_", $dataset);
// in the case that the user does not provide an output file name
if ($dataset == '') {
$dataset = "dist-output";
}
//dist.function.R takes number as argument for distance metric
if ($distance == 'Kruskal-Wallis') {
$distance = 1;
} else {
$distance = 2;
}
// string of arguments used by the RSCRIPT
// MUST BE IN THIS ORDER
$rArgs = "{$infile} {$clades} {$levels} {$metric} {$p} {$linkage} {$dataset} {$distance} {$tsv}";
$stdout = callR("callR.r", "{$rArgs}");
// $stdout contains all stdout of R code
// split $stdout at newlines
$stdout = explode("\n", $stdout);
// $stdout is an array. The last thing in the array is the full path
// of the actual file that we need
$file = $stdout[count($stdout) - 1];
// ** Download the zipped file ******************************
//copy($file, "/tmp/foo.zip" );
if (file_exists($file)) {
header("Content-type: application/zip");
header("Content-Disposition: attachment; filename={$dataset}.zip");
header("Pragma: no-cache");
header("Expires: 0");
ob_clean();
flush();
