If I understand you correctly you need to use <context:property-placeholder> and config like this:
<file:inbound-channel-adapter
channel="input"
directory="${dir}"
filename-pattern="${pattern}">
<poller fixed-delay="${fixedDelay}" time-unit="SECONDS"/>
</file:inbound-channel-adapter>
Where all those placeholders should be your program args, like this:
java myMain --dir=/usr/mydir --patter=myfile.name --fixedDelay=1000
UPDATE
However, no: you don't need <context:property-placeholder> - Spring Boot does that for you!
UPDATE 2
Sorry, you requirement is still not clear. Anyway how about this:
<int-event:inbound-channel-adapter channel="processFileChannel"
event-types="org.springframework.context.event.ContextRefreshedEvent"
payload-expression="new java.io.File('${filePath}')"/>
Where filePath is again an command line argument. And property placeholder from Spring Boot.
The <int-event:inbound-channel-adapter> is responsible to listen to ApplicationEvent. In this case we react to the ContextRefreshedEvent - a main event when you applicationContext is ready to do something.