If you have /usr/share/applications/application.desktop, change Exec=command to Exec=command %F in the file.
application: the name of application.
command: the name of application command.
sudo sed -i 's/Exec=command/Exec=command %F/' application.desktop
Then, you will be able to add the application to the list.
Please arrange the portion of Exec=command according to your application.desktop file.
It may be necessary to change MimeType=applications/php etc., if it is not still displayed.
Although it may be needlessness in this question, I consider that it may be effective in other applications.