Additions to create-genome-phylogeny

[elizabethmcd]

Integrating putative genome classifications with the Hug 2016 et al. TOL of genomes, highlighting input genomes

• Argument to download TOL genomes (bacteria, archaea, eukarya, all or some)
• Point to already downloaded TOL genomes directory or custom references directory
• Point to input references
• Make tree
• Highlight with metadata input genome for iTOL to visualize where they fall
• Also do this for highlighting on the ribosomal tree if a certain single marker falls anywhere

[elizabethmcd]

Put external data file for TOL accessions on github, read file within metabolisHMM create-genome-phylogeny workflow using urllib2 package to read the file and pass to ncbi-genome-download (which I believe can be used within python as arguments/package as well as the CLI)

[elizabethmcd]

just make this a demo, add arguments for refs vs input and highlight on tree