[Iska]

Здесь, как никогда, хорош будет PowerShell:

Код:

$sSourceFile = "C:\Песочница\022\0001.txt"
$sDestFile   = "C:\Песочница\022\0002.txt"

if(Test-Path -Path $sSourceFile) {
    Get-Content -Path $sSourceFile |`
        ForEach-Object -Process {
            ($_.Split(",") |`
                ForEach-Object -Process {
                    [System.Int32]$_.Trim()
                } | Sort-Object) -join ", "
        } | Set-Content -Path $sDestFile
} else {
    Write-Host -ForegroundColor Red "Can't find source file [$sSourceFile]"
}