To clarify, you wish to go from CASAVA 1.8+ ( Phred+33) quality scores
to the older version 1.3-1.7 ( Phred+64) quality scores?
This is possible with the "FASTQ Groomer" tool with the "Advanced
Please be aware that most, if not all, of Galaxy's tools are designed
work with Phred+33 scaled quality scores (e.g. "Sanger"). Illumina
output could be originally Phred+33 or Phred+64 depending on when it
generated and which software was used to post-process the data
1.3-1.7, 1.8+). Your source should be able to tell you what the data
content is. It can be tricky to guess, although the sequence headers
sometimes be a clue. The wikipedia link on the Groomer tool has a very
good explanation of this. The Groomer tool's output "Info" comments
also provide some feedback about valid quality score ranges vs the
options used, after processing.
For most users, when using the "FASTQ Groomer" tool, the goal is to
the data into "Sanger Phred+33" format. Even if the data is already in
"Sanger" format, the Groomer tool can be used to catch format
although directly changing the datatype to ".fastqsanger" is also OK
(for the tools that require this datatype in order for the dataset to
recognized; not all do).
* If the input is CASAVA 1.3-1.7, this is Phred+64, and the "Input
quality scores type: Illumina 1.3-1.7" should be used.
* If the input is CASAVA 1.8+, this is Phred+33, and the " Input FASTQ
quality scores type: Sanger" should be used.
Hopefully this helps,