So we have installed a local galaxy and most tools we use work perfectly fine. However, a tool I use for subsampling creates a gzipped file as output in the local galaxy. In the online galaxy a unzipped file is created.
Is there a possibility to unzip files on the local galaxy as the other tools in the workflow cannot deal with a zipped file? The online galaxy however seems to not have any issues.
Generally Galaxy supports compressed files, and if a tool requires uncompressed input Galaxy will decompress it on the fly and then supply to the tool. There is a bit of configuration involved so you can decide what formats you support compressed and which should always be decompressed.
fastqsanger will stay compressed in gz/bz2 unless you specifically set the datatype to an uncompressed one when creating/uploading. See auto_compressed_types config flag:
The tool is called: seqtk_sample. The issue is that it just creates the zipped files on the local galaxy but not on the online galaxy. If I use the same tool on the online galaxy, the file is not compressed.