The results from the tool are in your history as a dataset. Sometimes after running a tool you need to "refresh" the history panel using the double-circle icon at the top. Maybe that was the problem?
I see at least Cutadapt result dataset in your most current history. It has a correct fastq datatype (fastqsanger.gz) that is recognized by most tools as valid fastq input.
A few tools won't work with gz compressed data inputs - but most if not all of those are older/deprecated and should be avoided.
Which tool is ignoring these results as valid input?
- The tool I'm using does not recognize any input datasets. Why? https://galaxyproject.org/support/datatypes-and-tools/
Thanks and please share more details about what is going wrong if the above does not help enough. Jen, Galaxy team