When exporting files of the same type, I often have to rename the exported files before I can proceed with the next one as they share the same file name. It’d be great to enable users to rename the exported files in the qiime tools export command line.
We’re actually working on that right now! You should be able to export to different formats soon, so if you wanted to export a single file, you would say something like this (in the next release):
qiime tools export \
--input-path artifact.qza \
--output-path somewhere.txt \
--output-format let’s us know you want a particular file (and means we can name it now too) instead of just dumping the /data/ directory (which is why the filename always overlaps).