This makes the CLI a bit easier to use if you're in a hurry, since potentially generating a visualization can be as short as:
$ empress tree-plot -t tree.nwk -o viz
I also updated the README a bit to document this, and to make it a bit fancier in general. (One of the changes is consistently using hyphens in filenames for some of the early examples. I didn't modify the QIIME 2 tutorial since the filenames there [IIRC] were designed to be consistent with Q2's tutorial files, some of which have underscores instead of hyphens.)
Not all of the parameters in the standalone CLI have short equivalents (e.g. --filter-extra-samples will still have to be written out in full). I think this is reasonable, since arguably part of the rationale for many of these parameters is requiring the user to acknowledge e.g. "yes I recognize that I am asking the program to filter out certain samples right now".
This makes the CLI a bit easier to use if you're in a hurry, since potentially generating a visualization can be as short as:
I also updated the README a bit to document this, and to make it a bit fancier in general. (One of the changes is consistently using hyphens in filenames for some of the early examples. I didn't modify the QIIME 2 tutorial since the filenames there [IIRC] were designed to be consistent with Q2's tutorial files, some of which have underscores instead of hyphens.)
Not all of the parameters in the standalone CLI have short equivalents (e.g.
--filter-extra-sampleswill still have to be written out in full). I think this is reasonable, since arguably part of the rationale for many of these parameters is requiring the user to acknowledge e.g. "yes I recognize that I am asking the program to filter out certain samples right now".