My space is 54% occupied and the message displayed on trying to select flattened collection is as follows:
What is going wrong?
Try these:
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Make sure that the history with the data is the active history (User → Histories). Then click into something else (maybe another tool), then click back on this tool to refresh the tool form. A shift-reload for the entire webpage can also work.
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Double check that the datasets you are trying to select have the datatype fastqsanger or fastqsangergz assigned. When read files are in a collection folder, the top level of the folder will expose that metadata in the history view. Other datatypes you might need to click into the collection to review this.
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Remember that if you want to input a collection of files, then you’ll need to use the “folder” icon to tell Galaxy to look for a collection folder. If the tool form does not “see” data, there is probably a reason. Most people should avoid dragging and dropping.
Next time you Upload fastq files, let Galaxy autodetect the datatype. That guess interprets the quality score scaling and compression state. More details → Getting Data into Galaxy
If that doesn’t help, you can try sharing more screenshots about how those three items are set up, and explain more about what you expect versus behavior. The server might matter so include the URL please. Thanks! 