progress
Merge branch 'master' of github.com:qiime/American-Gut into license
cleaned it up...
removed files not relevant to this branch
removed extraneous column
Merge pull request #5 from wasade/hmp_metadata_fix

removed extraneous column
Merge pull request #4 from wasade/license

License
Add option to preserve or not the Z position

Objects can now preserve or not their position in the Z axis, if the
position is preserved then when the "magnified" object is added to the
global file, the object will be positioned exactly where the
"non-magnified" object was. In any other case the object will simply
retain the (x, y) positioning and will be drawn at the very end of the
global file, making it such that it will appear infront of any of the
other objects that were in the scene.
Add tests for cases where Z is not preserved
Merge pull request #7 from ElDeveloper/replacement_ontop

Replacement ontop
Modify regular expression in format.py
Change regex to make it </path> inclusive
Add check to stdout and stderr for the subprocess

There's sometimes useful information that inkscape gives back in case
something is failing.
Merge pull request #8 from ElDeveloper/regex

:cake:
Add code to remove background rect from print

The background rect object that was found in the SVG formatted files was
there given the fact that Emperor allows you to set the background color
for the print. If we leave this object in there we cannot use Inkscape's
fit to drawing area functionality.
Change inkscape command call to crop the prints

Prints are now cropped to be the size of the area these are using only.
Merge pull request #10 from ElDeveloper/print_cropping

Print cropping
I am adding the LaTeX files.
These are the accessory files for template.tex to work:

macros_xxx.tex - should be in the same directory as template.tex
pdfs/ - this directory containing image files should be in same directory as template.tex
    - legend files should be same for every individual, but legends 2 and 3 still need tweaking
    - ovals file should be same for every individual, but it's exact postitioning will change based on final figure1
    - headerbw should be replaced with the original from Adobe document
    - figure4 should be done with Helvetica to match legends

IMPORTANT: For fonts to work, template.tex must be run with LuaLaTeX (or possibly XeTeX) preferably on a Mac that has Futura font installed.
Renamed figureX.pdf to figmockupX.pdf