I am adding the code that works as intended for future reference and an exact answer to the question:
<?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">
<Product Id="guid_here" Name="WixSingleSetupExample" Language="1055"
Version="1.0.0.0" Manufacturer="Can Yucel" UpgradeCode="guid_here">
<Package InstallerVersion="200" Compressed="yes" InstallScope="perMachine" />
<MajorUpgrade DowngradeErrorMessage="A newer version of [ProductName] is already installed." />
<MediaTemplate />
<Feature Id="ProductFeature" Title="WixSingleSetupExample" Level="1">
<ComponentGroupRef Id="ProductComponents" />
<ComponentRef Id="ProgramMenuDir"/>
</Feature>
</Product>
<Fragment>
<Directory Id="TARGETDIR" Name="SourceDir">
<Directory Id="DesktopFolder" Name="Desktop" />
<Directory Id="ProgramMenuFolder" Name="Programs">
<Directory Id="ApplicationProgramsFolder" Name="WixSingleSetup">
<Component Id="ProgramMenuDir" Guid="guid_here">
<RemoveFolder Id="ProgramMenuDir" On="uninstall"/>
<RegistryValue Root="HKCU" Key="Software\[Manufacturer]\WixSetup"
Type="integer" Value="1" Name="installed" KeyPath="yes" />
</Component>
</Directory>
</Directory>
<Directory Id="ProgramFilesFolder">
<Directory Id="INSTALLFOLDER" Name="WixSingleSetupExample" />
</Directory>
</Directory>
</Fragment>
<Fragment>
<ComponentGroup Id="ProductComponents" Directory="INSTALLFOLDER">
<!-- TODO: Remove the comments around this Component element and the
ComponentRef below in order to add resources to this installer. -->
<Component Id="ProductTextFile">
<File Source="blankText.txt" KeyPath="yes">
<Shortcut Id="desktopShortcut" Advertise="yes" Directory="DesktopFolder"
Name="WixSingleSetup Help" WorkingDirectory="INSTALLFOLDER"
Icon="icon1.txt" IconIndex="0">
<Icon Id="icon1.txt" SourceFile="blankText.txt" />
</Shortcut>
<Shortcut Id="startMenuShotcut" Directory="ApplicationProgramsFolder"
Name="WiXSingleSetup Help" WorkingDirectory="INSTALLFOLDER"
Icon="icon2.txt" IconIndex="0" Advertise="yes">
<Icon Id="icon2.txt" SourceFile="blankText.txt"/>
</Shortcut>
</File>
</Component>
</ComponentGroup>
</Fragment>
</Wix>