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_file

Path to read otu table

-m, --mapping_file

Path to read mapping file

-t, --tree_file

Path to read tree

[OPTIONAL]

-o, --output_dir

The output directory [default: None]

-p, --prefs_file_dir

Path to prefs file

-w, --web

Web codebase jnlp flag [default: False]

-u, --url_path

Url path

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.txt -m mapping_file.txt -t otus.tre -o my_data