setBatchMode(true);
dir=getDirectory("Choose an Input Directory");
print(dir);
list = getFileList(dir);
saveloc = getDirectory("Choose Ouput Directory");

for (i=0; i<list.length; i++) {
     if (endsWith(list[i], ".tif")){
               print(i + ": " + dir+list[i]);
             open(dir+list[i]);
             imgName=getTitle();
         run("Split Channels");
         selectWindow("C1-"+imgName);
         saveAs("Tiff", saveloc + "C1-"+imgName);
         close();
         selectWindow("C2-"+imgName);
         saveAs("Tiff", saveloc + "C2-"+imgName);
         close();
         selectWindow("C3-"+imgName);
         saveAs("Tiff", saveloc + "C3-"+imgName);
         close();
         run("Close All");
     } else {
      }
}

run("Image Sequence...", "open=[saveloc] file=C1 use");");
saveAs("Tiff", saveloc+"FullStackC1.tif");
run("Close All");

run("Image Sequence...", "open=[saveloc] file=C2 use");");
saveAs("Tiff", saveloc+"FullStackC2.tif");
run("Close All");

run("Image Sequence...", "open=[saveloc] file=C3 use");");
saveAs("Tiff", saveloc+"FullStackC3.tif");
run("Close All");

list = getFileList(dir);
for (i=0; i<list.length; i++) {
     if (startsWith(list[i], "C"))
File.delete(dir+list[i]);
}

Dialog.create("Progress");
Dialog.addMessage("Complete!");
Dialog.show;

setBatchMode(false);