ccrsilib.lua

local function outputSides(box, north, east, south, west)
    box.setOutput("top", false)
    box.setOutput("bottom", false)
    box.setOutput("north", north)
    box.setOutput("east", east)
    box.setOutput("south", south)
    box.setOutput("west", west)
end

return { outputSides = outputSides }

minelib.lua

local function hasTag(item, tag)
    local tags = item["tags"]
    if not tags then
        return false
    end
    if tags[tag] then
        return true
    else
        return false
    end
end

return { hasTag = hasTag }

operatorlib.lua

local function eq(val1, val2)
    return val1 == val2
end

local function neq(val1, val2)
    return val1 ~= val2
end

return { eq = eq, neq = neq }

run.lua

lualib = require("mylualib")
operator = require("operatorlib")
rsilib = require("ccrsilib")
minelib = require("minelib")

inputChestName = "minecraft:barrel_0"
inputChest = peripheral.wrap(inputChestName)
hopperName = "minecraft:hopper_0"
hopper = peripheral.wrap(hopperName)
outputChestName = "abnormals_core:chest_8"
outputChest = peripheral.wrap(outputChestName)
interfaceName = "refinedstorage:interface_1"
interface = peripheral.wrap(interfaceName)
rsiName = "redstoneIntegrator_3"
rsi = peripheral.wrap(rsiName)

function findItem(inv, itemName, op)
    for slot, item in pairs(inv.list()) do
        if op(item.name, itemName) then
            return slot
        end
    end

    return -1
end

function findByTag(inv, tag)
    for slot, item in pairs(inv.list()) do
        itemDetail = inv.getItemDetail(slot)
        if minelib.hasTag(itemDetail, tag) then
            return slot
        end
    end

    return -1
end

function processInput(inv)
    waterBucketSlot = findItem(inv, "minecraft:water_bucket", operator.eq)
    if waterBucketSlot > -1 then
        print("pushing water bucket")
        inv.pushItems(hopperName, waterBucketSlot)
        return
    end

    nonSeedSlot = findItem(inv, "minecraft:wheat_seeds", operator.neq)
    if nonSeedSlot > -1 then
        print("pushing non-seed")
        inv.pushItems(hopperName, nonSeedSlot)
        return
    end

    seedSlot = findItem(inv, "minecraft:wheat_seeds", operator.eq)
    if seedSlot > -1 then
        print("pushing wheat seed")
        inv.pushItems(hopperName, seedSlot)
        return
    end
end

function processOutput(inv)
    for slot, item in pairs(inv.list()) do
        if item.name == "minecraft:wheat_seeds" then
            inv.pushItems(hopperName, slot)
            return
        end

        itemDetail = inv.getItemDetail(slot)
        if minelib.hasTag(itemDetail, "botania:petals") then
            inv.pushItems(hopperName, slot)
            return
        end
        
        isFlower = minelib.hasTag(itemDetail, "botania:special_flowers")

        if isFlower then
            print("starting redstone pulse")
            rsilib.outputSides(rsi, false, false, true, false)
        end

        print(("pushing to output: %s"):format(item.name))
        inv.pushItems(interfaceName, slot)

        if isFlower then
            print("ending redstone pulse")
            rsilib.outputSides(rsi, false, false, false, false)
        end
        return
    end
end

while true do
    processInput(inputChest)

    processOutput(outputChest)
end