is there a way to clean fastq files (filter Poly-A etc.) with Galaxy?
Haven't found anything so far. Also if you generally know good tools
Have seen lots of stuff for fasta and qual files but not for fastq.
The tools under "NGS: QC and manipulation -> Generic FASTQ
should be able to help, in particular "Manipulate FASTQ reads on
attributes" will allow you to enter a regular expression that could
poly-A tails (the same way a perl script could, for example). The tool
has link to more documentation about how to construct expressions).
if you know the length of the insert sequence you want to retain,
"Filter FASTA" would be a good choice.
Please give these a try and let us know if we can help more.