There's a bounty for this right? i spent nearly two full days at this

code/modules/reagents/chemistry/machinery/chem_master.dm

@@ -221,7 +221,8 @@
 		var/to_container = params["to"]
 		// Custom amount
 		if (amount == -1)
-			amount = text2num(input(
+			amount = text2num(tgui_input_num(
+				usr,
 				"Enter the amount you want to transfer:",
 				name, ""))
 		if (amount == null || amount <= 0)
@@ -256,7 +257,7 @@
 		// Get amount of items
 		var/amount = text2num(params["amount"])
 		if(amount == null)
-			amount = text2num(input(usr,
+			amount = text2num(tgui_input_num(usr,
 				"Max 20. Buffer content will be split evenly.",
 				"How many to make?", 1))
 		amount = clamp(round(amount), 0, 20)
@@ -285,7 +286,7 @@
 		if(vol_each_text == "auto")
 			vol_each = vol_each_max
 		if(vol_each == null)
-			vol_each = text2num(input(usr,
+			vol_each = text2num(tgui_input_num(usr,
 				"Maximum [vol_each_max] units per item.",
 				"How many units to fill?",
 				vol_each_max))

code/modules/reagents/chemistry/machinery/chem_synthesizer.dm

@@ -30,7 +30,7 @@
 				beaker = null
 				. = TRUE
 		if("input")
-			var/input_reagent = replacetext(lowertext(input("Enter the name of any reagent", "Input") as text|null), " ", "") //95% of the time, the reagent id is a lowercase/no spaces version of the name
+			var/input_reagent = replacetext(lowertext(tgui_input_text(usr, "Enter the name of any reagent", "Input")), " ", "") //95% of the time, the reagent id is a lowercase/no spaces version of the name
 
 			if (isnull(input_reagent))
 				return