view PaDEL/temp.dir/padel.pl.orig @ 0:a4a2ad5a214e draft default tip

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$input=$ARGV[0];
$all_coordinates=$ARGV[1];
$fingerprint=$ARGV[2];
$output=$ARGV[3];
system("mkdir tmp");
system("cp $input tmp/file.sdf");
$command="/usr/bin/java -jar ~/galaxy-dist/tools/PaDEL/PaDEL-Descriptor.jar -dir tmp -2d -file $output";
if($all_coordinates == 1 && $fingerprint==0)
{
 $command = $command." -3d";
}
elsif($fingerprint==1 && $all_coordinates==0)
{
$command = $command." -fingerprints";
}
elsif ($all_coordinates==1 && $fingerprint==1)
{
$command = $command." -3d -fingerprints";
}
system("$command");