i want to perform the taxonomy to krona file , but the file options shos no mothur files to be selelcted and i uploaded the cons.taxonomy file
Welcome, @yasmeen_hisham
An input on a tool form is performing a filter against the datasets in the active history.
- To review what that filter is, click on the accepted formats toggle.
- Then click to expand your dataset.
- When the datatype formats “match”, a file becomes available to select.
You can reassign a datatype format if you think it is wrong. You can also convert to a different format. Sometimes you will need to process data through another tool to create new content.
Scroll all the way down on the tool form to find discussion in the Help section about a tool (right above where you found the link to this forum). If you file matches that content, then you can be pretty safe assigning the correct datatype format. You can also review the associated tutorials for more examples.
So, why do this? Informing the tool automatically about the type of file to process can be important for those tools that can accept multiple types. It is also a simple sanity check to make sure an input file has any hope of running through the target tool! You’ll still need to make sure the content inside the file is a scientific fit.
Resources
- Single file
- Multiple files in a collection folder
Letting Galaxy “guess” the format when first uploading is usually a good idea. If the guess is wrong, especially for common datatypes, that can be an important clue about a partial data load, corrupted file, and similar. But if you confirm the guess was just wrong, or rather not specific enough (you probably have text or tabular currently, or some other tabular-type assigned), you can make a direct adjustment.
Hope this helps but you can share more back, including screenshots, for any followup questions. Let us know if you get this working, too! 
Thank you so much that as very helpful, can I ask you how can I do the lefse pie chart to compare between groups?
There are two choices for Lefse at the UseGalaxy servers. Search the tool panel with the tool name to find those.
The best advice I have for the scientific decisions is to review the linked documentation at the bottom of the tool form. Those are really comprehensive, and will help you to understand what the short tips on the form are about. Then, just try it a few different ways, since actual data usually helps, too. Or, try the sample data the authors host.