Sounds like you want to create an IPA on the command line from an existing xcarchive. Since Xcode 7, the preferred way to do this is (from man xcodebuild):
xcodebuild -exportArchive -archivePath xcarchivepath -exportPath destinationpath -exportOptionsPlist path
So in your case:
xcodebuild -exportArchive -archivePath MyApp.xcarchive -exportPath MyApp.ipa -exportOptionsPlist exportOptions.plist
exportOptions.plist is a PLIST file that contains various parameters configuring the IPA export. See xcodebuild -help for all available options. You'll have to at least specifiy an entry for method (app-store, ad-hoc, enterprise etc. - defaults to development). If you just want to export for App-Store distribution, the file should look like this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>method</key>
<string>app-store</string>
</dict>
</plist>