Here is a quick script to use to upload Modules to Azure Automation.

Switch-AzureMode AzureResourceManager
$cred = Get-Credential 
Add-AzureAccount -Credential $cred

Select-AzureSubscription -SubscriptionId <SubscriptionID>
$ResourceGroup = Get-AzureResourceGroup -Name "IaaSAutomation"
$MyAutomationAccount = $ResourceGroup | Get-AzureAutomationAccount -Name "IaaSAutomation"
$MyAutomationAccount | New-AzureAutomationModule -name "xWebAdministration"  -ContentLink "https://github.com/PowerShell/xWebAdministration/archive/1.7.0.0-PSGallery.zip" 
$MyAutomationAccount | New-AzureAutomationModule -name "xPhp"  -ContentLink "https://github.com/PowerShell/xPhp/archive/1.1.0.0-PSGallery.zip" 
$MyAutomationAccount | New-AzureAutomationModule -name "xWordPress"  -ContentLink "https://github.com/PowerShell/xWordPress/archive/1.1.0.0-PSGallery.zip" 
$MyAutomationAccount | New-AzureAutomationModule -name "xMySQL"  -ContentLink "https://github.com/PowerShell/xMySql/archive/1.1.0.0-PSGallery.zip"