Php script to upload file from client's computer to server

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PHP

So before I tell you my specific issue, what I am trying to create is a C# application that will manage user's shared presets for a guitar pedal. So in order to do this, I need the ability to upload files from the user's computer, to my server/hosting.

I could use built in C# libraries to make an ftp connection and upload files to my server, but then my precious information would be exposed and vulnerable to being seen regardless of my attempts to encrypt/obfuscate the code.

So in order to protect my information I want to create a php script to do the uploading, but I need to invoke the php script from my C# application. I can easily make webrequests in C# to php pages, which I am doing now to serve the data from my database, but uploading files to my server is quite different.

Anyone know how I might do this?