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

code/modules/reagents/chem_wiki_render.dm

@@ -17,7 +17,7 @@
 
 
 	var/prefix = "|Name | Reagents | Reaction vars | Description | Chem properties |\n|---|---|---|-----------|---|\n"
-	var/input_reagent = replacetext(lowertext(input("Input the name/type of a reagent to get it's description on it's own, or leave blank to parse every chem.", "Input") as text), " ", "") //95% of the time, the reagent type is a lowercase, no spaces / underscored version of the name
+	var/input_reagent = replacetext(lowertext(tgui_input_text(src, "Input the name/type of a reagent to get it's description on it's own, or leave blank to parse every chem.", "Input")), " ", "") //95% of the time, the reagent type is a lowercase, no spaces / underscored version of the name
 	if(input_reagent)
 		var/input_reagent2 = find_reagent(input_reagent)
 		if(!input_reagent2)

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

code/modules/reagents/reagent_containers.dm

@@ -47,7 +47,7 @@
 	set name = "Set Transfer Amount"
 	set category = "Object"
 	set waitfor = FALSE
-	var/N = input("Amount per transfer from this:","[src]") as null|anything in possible_transfer_amounts
+	var/N = tgui_input_list(usr, "Amount per transfer from this:","[src]", possible_transfer_amounts)
 	if(N)
 		amount_per_transfer_from_this = N
 		to_chat(usr, "<span class='notice'>[src]'s transfer amount is now [amount_per_transfer_from_this] units.</span>")

code/modules/reagents/reagent_containers/borghypo.dm

@@ -122,7 +122,7 @@ Borg Hypospray
 	log_combat(user, M, "injected", src, "(CHEMICALS: [english_list(injected)])")
 
 /obj/item/reagent_containers/borghypo/attack_self(mob/user)
-	var/chosen_reagent = modes[reagent_names[input(user, "What reagent do you want to dispense?") as null|anything in reagent_names]]
+	var/chosen_reagent = modes[reagent_names[tgui_input_list(user, "What reagent do you want to dispense?", "", reagent_names)]]
 	if(!chosen_reagent)
 		return
 	mode = chosen_reagent