make_tep.py – Makes TopiaryExplorer project file

Description:

This script makes a TopiaryExplorer project file (.tep) and a jnlp file with the data location preloaded.

WARNING: The jnlp file relies on an absolute path, if you move the .tep file, the generated jnlp will no longer work. However, you can still open the .tep file from your normal TopiaryExplorer install.

Usage: make_tep.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

Path to the input OTU table (i.e., the output from make_otu_table.py)

-m, --mapping_fp

The mapping filepath

-t, --tree_fp

Path to tree

[OPTIONAL]

-o, --output_dir

Path to the output directory

-p, --prefs_file_fp

Path to prefs file

-w, --web_flag

Web codebase jnlp flag [default: False]

-u, --url

Url path for the tep file. Note: when passing this flag, it will overwrite the supplied OTU table, Mapping and Tree files.

Output:

The result of this script is written to a .tep file and a .jnlp file, both with the name supplied by -o

Example:

Create .tep file and .jnlp file:

make_tep.py -i otu_table.biom -m Fasting_Map.txt -t rep_set.tre